In this study, three cotton near isogenic lines with different fiber colors, green cotton, brown cotton and white cotton, were selected as materials to study the changes of physiological characteristics of main stem functional leaves in the whole growth stages, and the correlation between physiological indexes and yield factors was analyzed. The results showed that the net photosynthetic rate of two colored cottons in the whole growth stages was lower than that of white cotton, and the total chlorophyll content, sucrose synthetase and sucrose phosphate synthetase activity of colored cotton were lower than that of white cotton except for the boll opening stage. The net photosynthetic rate was positively correlated with the number of boll per plant and the weight of boll,and yield per plant. The chlorophyll contentwas positively correlated with boll weight and yield per plant.Sucrose phosphate synthetase activity was positively correlated with the weight of boll and yield per plant. The results of this study will provide a theoretical basis for the breeding of high-yield varieties of colored cotton.