[Aim] A very important ecological task before introducing a new type of genetically modified cotton for large-scale commercial applications is to evaluate its biosafety. The secondary metabolism of cotton may be affected by the new gene introduced and even lead to a series of ecological effects. The physiological changes in the cotton cultivar are also an important part of safety evaluation of transgenic plants.[Method] This paper compares the transgenic Cry1Ac+Cry2Ab cotton and Cry1Ac cotton with non-transgenic cotton in selected parameters during different critical developmental (seedling, budding and flowering and boll forming stages) periods. These parameters include the fresh and dry mass and ratio of dry mass to fresh mass of cotton leaf. Activities of important enzymes like SOD (super oxide dismutase), CAT (catalase), POD (peroxidase), APX (ascorbate peroxidase) and GR (glutathione reductase) were measured. We also measured the amounts of protein, ammonia nitrogen, soluble sugars, and secondary metabolites like gossypol and tannins. The number of individuals and species in different layers were investigated.[Result] During the budding, flowering and boll forming, the cotton leaf fresh mass, dry mass, their ratio, protein content and soluble sugars all showed first an increasing, then a decreasing trend. Activities of SOD and POD enzyme significantly increased in the boll forming stage, however, the other enzymes, CAT, APX and GR did not change significantly during the three periods. Ammonia nitrogen had no obvious change. Tannin contents gradually increased, while the gossypol content did not change significantly. Accumulation of dry matter, enzyme activities, nutrient content, and the amounts of secondary metabolites had no significant difference between the three kinds of cotton leaves. The number of big bolls was highest in Cry1Ac+Cry2Ab cotton, followed by Cry1Ac cotton and non-transgenic cotton; the number of small bolls was lowest in Cry1Ac cotton, followed by Cry1Ac+Cry2Ab, then non-transgenic cotton. The total number of insect individuals in the insect community and pest sub-community showed that Cry1Ac+Cry2Ab cotton < Cry1Ac cotton < non-transgenic cotton fields. However, the total number of individuals in the natural enemy sub-community was not significantly different. The number of species in the pest and natural enemy sub-communities between the three kinds of cotton varieties had no obvious difference.[Conclusion] Accumulation of dry matter, yield, the amount of biochemical substances and enzyme activities in the transgenic Cry1Ac+Cry2Ab cotton showed differences in the three different development stages. The same parameters between the transgenic and non-transgenic cotton had no obvious differences. We registered no difference in the abundance of the censused arthropod community.