A set of 403 accessions tea genetic resources were selected from China National Germplasm Hangzhou Tea Repository (CNGHTR) to test the purine alkaloids content of spring and autumn in two years using HPLC. It revealed the caffeine content of tea genetic resources were relatively stable between years or seasons, while the theobromine content had a significant variation in spring. The caffeine content of more than 93% resources varied from 25.0 to 45.0 mg/g. Caffeine content had a significant difference in the three varieties of Camellia sinensis (L.) O. Kuntze, and that of assamica variety in autumn was significantly higher than the spring’s. The variation of caffeine among different provinces had been investigated. It had a significant difference in the contents, and Guangdong and Yunnan had higher coefficient of variation (CV) and diversity indices (H’). Moreover, 6 specific tea accessions were screened out, including 3 high caffeine, 1 low caffeine and high theacrine, 2 low caffeine and high theobromine accessions, respectively.