Lakes are one of the main ecosystems for carbon fixation; however, the microbial community for carbon fixation in the lakes of the Tibetan Plateau have rarely been reported. In this study, the Nam Co Lake was chosen to study the abundance of cbbL ID genes and their composition using quantitative PCR and a clone library method. We also discuss their relationship with environmental parameters. The results showed that there was a high abundance of the cbbL ID gene in the Nam Co Lake, and there was an increasing trend from the surface to the bottom, and the highest amount was in the bottom sample of T2 (6.37×10⁸ copies/L water). The community was mainly composed of Stramenopiles and Haptophyceae, and a few Cyanobacteria and Cryptophyta appeared on individual layers. The Stramenopiles group had a higher diversity (including 7 classes and 13 families) than that of the other groups, and there was only 1 family of another taxa. A correlation analysis showed there was a significant negative correlation (P<0.01) of the occurrence frequency of Stramenopiles and Haptophyceae. Water depth and pH had a significant correlation with cbbL ID gene abundance (P<0.05, P<0.01, respectively). Chlorophyll content had a significant correlation with the occurrence frequency of Stramenopiles and Haptophyceae.