rectory of Lampeter Velfrey, Pembrokeshire (1661–5), and in 1661 was made chaplain to the Duke of York, whom he attended in his voyage to Dunkirk and in one of his engagements with the Dutch. Through the duke's interest he was appointed dean of Worcester on 25 Nov. 1665, and, though a stranger, he is said to have ‘gained the affections of all the gentlemen of that county, particularly the Duke of Beaufort, Lord Windsor (afterwards Earl of Plymouth), and Sir John Pakington’ (1620–1680), the last of whom presented him on 12 June 1670 to the rectory of Hampton Lovett, Worcestershire.
In November 1677 he was appointed bishop of St. David's, but was allowed to hold the deanery of Worcester in commendam. His predecessor, William Lucy, had apparently regarded him as his most likely successor as early as 1670, when he enjoined Thomas to complete the private chapel commenced by Laud at Abergwili, ‘if I finish it not in my life’ (Hutton, Laud, p. 22). Excepting John Lloyd, who died (February 1686–7) within a few months of his consecration, Thomas was the only Welshman appointed to the see of St. David's in the seventeenth century, and he was ‘the one bishop who, during the whole of that period, seems to have thoroughly identified himself with the interests of his diocese’ (Bevan, Diocesan History of St. David's, p. 196). He was popular with the gentry and clergy, whose sufferings he had shared during the Commonwealth. He was well acquainted with the Welsh language, in which he often preached in various parts of his diocese. It was through his instrumentality that Stephen Hughes, the puritan divine, obtained the necessary authority for publishing the third part of Vicar Prichard's Welsh songs in 1670, and he is also said to have supported Hughes and Thomas Gouge in bringing out an octavo edition of the Welsh Bible, either in 1671 or 1677 (cf. Rowlands, Cambrian Bibliography, pp. 197–8, 200, 213; Canwyll y Cymry, ed. Rice Rees, 1867, p. 320). He began to repair the episcopal palaces at Brecon and Abergwili, and revived a scheme of Bishop Barlow's for removing the see from St. David's to Carmarthen (Jones and Freeman, St. David's, p. 333; cf. Bevan, Diocesan History of St. David's, p. 188).
In 1683 he was translated to the see of Worcester, his election thereto being confirmed on 27 Aug. Here he indulged in such lavish, if not excessive, charity and hospitality as to considerably impoverish his family. ‘The poor of the neighbourhood were daily fed at his door;’ he contributed largely to the support of the French protestants; and during his visitations he entertained the clergy at his own charge, devoting the customary fees to the purchase of books for the cathedral library. In July 1684 he entertained the Duke of Beaufort on his official progress through Wales and the marches (Dineley, Beaufort Progress, p. 29), and on 23 Aug. 1687 James II also stayed at the palace, where the decorations caused him to say to the bishop, ‘My lord, this looks like Whitehall.’ He, however, staunchly adhered to the protestant cause, and is said to have been cited in June 1687 before the ecclesiastical commission for refusing orders to several papists who declined to take the usual oaths (Luttrell, Brief Relation, i. 405). He also refused to distribute among his clergy the declaration of indulgence by James in May 1688. He was one of the bishops who absented themselves from the convention called in the following January, after the landing of William, and he subsequently refused to take the oath of allegiance, whereupon he was suspended, and would have been deprived but for his death on 25 June 1689. Two days before his death he sent for his dean, Dr. George Hickes [q. v.], and made to him a solemn declaration, which was afterwards much quoted by the nonjurors, saying, ‘I think I could burn at a stake before I took this oath’ (Memoirs of the Life of George Kettlewell, 1718, pp. 198–203; Carter, Life of Kettlewell, pp. 105, 126). He was buried, at his own request, at the north-east corner of the cloisters, near the foot of the choir steps.
He married, about 1638, Blanche, daughter of Peter Samyne, a Dutch merchant, of Lime Street, London. She died on 3 Aug. 1677, and was buried in Worcester Cathedral, having borne him four sons and four daughters. The eldest surviving son, John, was father of William Thomas (1670–1738) [q. v.], the antiquary.
By his will the bishop made numerous charitable bequests, including 100l. to the poor of Worcester, but his whole estate amounted to only 800l. His portrait, engraved by T. Sanders ‘from an original picture,’ is given in Nash's ‘Worcestershire’ (vol. ii. App. p. 160).
In December 1655, in reply to the friendly challenge of a dissenting minister, Thomas wrote, while still at Laugharne, ‘An Apology for the Church of England in point of separation from it,’ but the work was not published till 1679 (London, 8vo). Three of his sermons were issued separately (in 1657, 1678, and 1688). There were also