Russell W. Thornton joined the Department of Agriculture of the Cape Colony in March 1906 as an agricultural assistant, a post that was renamed government agriculturalist in 1908. In 1907 he was seconded to the Division of Entomology to take charge of the first locust campaign and in 1909 again acted as chief locust officer for the campaign of that year. However, much of his time between 1906 and 1910 was spent conducting crop and pasture research at the Robertson Experiment Station, on which he published several articles in the Agricultural Journal of the Cape of Good Hope. The first of these dealt with the feeding values of Karoo bushes compared with cultivated crops (1908, Vol. 33, pp. 60-65). The next year he reported his research on the relative rust resistance and yields of various varieties of wheat, oat and barley (1909, Vol. 35, pp. 65-73). He found Gluyas and Rieti to be the best wheats, Algerian the best oats, and Cape Six Row the best barley variety. Around this time he selected three types of wheat from material produced by E.A. Nobbs*, naming them Union A, Union B, and Union C, from which J.H. Neethling* later obtained his famous high-yield, early-maturing Union selections. Thornton published his part of the work in "Wheat hybridisation; a report on the first South African wheat hybrids" (1910, Vol. 36). Later that year he described his experiments on "Soil evaporation" (1910, Vol. 36, pp. 342-347), in which he found that cultivation of the soil conserves moisture, followed by further results of his irrigation, evaporation and dry land experiments (1910, Vol. 36, pp. 547-553). Later he also contributed an article on "The tobacco industry in the Western Province" to the Agricultural Journal of the Union of South Africa (1911, Vol. 2, p. 102).
At the annual congress of the South African Association for the Advancement of Science held in Bloemfontein in 1909 Thornton contributed a paper on "Maize breeding" which was published in the Association's Report for that year (pp. 60-63). He became a member in 1910 and subsequently contributed papers on "Agricultural education" (1911, pp. 203-208) and "The ostrich feather industry in South Africa" (1915, pp. 272-279).
While retaining his title of government agriculturalist Thornton was appointed in 1910 as the first principal of the Grootfontein School of Agriculture, which opened near Middelburg, Cape Province, in February 1911 with 42 students and a staff of 16 professional and technical officials. Soon after his appointment the government sent him on a tour to England, continental Europe, Canada, the United States and Australia to visit various agricultural colleges and experimental stations, and to Nigeria and Sudan in charge of the so-called Ostrich Expedition. He was also sent to South West Africa (now Namibia) to find a variety of Afrikaner sheep with short, smooth hair instead of wool, for experimental cross-breeding with Karakul sheep. On this expedition "Scotty Smith" (George St L G Lennox*) accompanied him as guide.
Thornton remained principal at Grootfontein until the end of 1923, when he was succeeded by M.J. Joubert. That same year he published a small pamphlet, in both English and Afrikaans, on The economics of irrigation farming: The small holding (Cape Town, 1923, 15p). He visited the Argentine and Uruguay in 1928, mainly to investigate the cattle industry. Subsequently he became Director of Native Agriculture for the Union of South Africa (1929-1934) and in 1930-1931 was a member of the first Wool Council. In 1934 he was transferred to the post of Director of Agriculture of Basutoland (now Lesotho) and agricultural advisor to the High Commissioner of Basutoland, Swaziland and British Bechuanaland.