Differently expression proteins under high-temperature and drought stress were screened to investigate how stress affected the insecticidal protein content. These stresses decrease insecticidal protein, so the goal of this study was to provide a theoretical reference for maintaining the insect resistance of Bt cotton. The effect of high-temperature and drought stress on differently expression protein in Bt cotton cultivar Sikang 3 was investigated using a label-free quantitation method. Two treatments [40% field capacity and 38 degrees C (HD) and 70% field capacity and 32 degrees C (CK)] were imposed in a controlled environment. The results showed that high-temperature and drought significantly degraded insecticidal protein content in bolls, with a decrease of 65.2 ng/g fresh weight (FW) compared to CK. The analysis of differently expression proteins with a label-free quantitative proteomic approach showed that 83 proteins were significantly up-regulated, but 104 proteins were significantly down-regulated (Ratio > +/- 2,pvalue < 0.05) compared with CK. In addition, 122 new proteins were detected and 167 proteins were not detected. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that 14 KEGG pathways, in which the difference expression proteins were enriched, were significantly affected and three KEGG pathways (carbohydrate digestion and absorption, protein export and protein processing in endoplasmic reticulum) were related to protein synthesis. In the carbohydrate digestion and absorption pathway, the capacity of starch hydrolysis for HD increased, while the capacity to phosphorylate the hexoses, fructose and glucose decreased. In protein export pathway, the synthesis of peptide for HD was not significant affected, while the process of peptide transferred into the endoplasmic reticulum was confined. In the protein processing in endoplasmic reticulum pathway, the capacity of ubiquitin-mediated proteolysis increased.