Field experiments were conducted in Xinping, Yuxi and Xundian to investigate the yield and functional components and their environmental variation among different rice genotypes including 14 cultivars from Yunnan. The results showed that mean rice yield, valid spike number and seed setting rate in Xundian were significantly higher than those in Xinping and Yuxi, and those in Xinping were the lowest. Spikelets per panicle in Yuxi was significantly higher than that in Xinping and Xundian, while 1 000-grain weight showed no significant difference among three eco-sites. Path analysis showed that grain yield was mainly influenced by spikelets per panicle, valid panicles and seed setting rate. The grain yield and yield components and functional elements were significantly or very significantly affected by genotype (G), environment (E) and their interaction (G×E). The yield, valid panicles, spikelets per panicle and seed setting rate were mainly regulated by environment, while grain weight mainly by genotype. The γ-aminobutyric acid (GABA) was impacted by eco-environment, while total flavonoids and alkaloids by genotype and G×E interaction, and resistant starch (RS) by genotype. The GABA and alkaloids of brown rice were the highest in Xinping, and similar in Yuxi and Xundian. Total flavonoids were the highest in Yuxi, the lowest in Xundian. There was no significant difference in RS of brown rice among three eco-sites.