Antheraea pernyi (A.pernyi) pupa is rich in high quality protein, which is a kind of food raw material with high development and utilization value. The effects of different pH values on the gel properties of A. pernyi pupae flour and the thermal aggregation of protein molecules were studied by texture analyzer, rheometer and confocal laser scanning microscope. The results showed that the gel network formed at pH 7 was relatively continuous and uniform, and the water retention of gel was the highest (51.67%±0.79%, P<0.05). At pH 9, A. pernyi pupae flour had the least critical gel mass fraction (8%), the highest gel hardness (41.67N±3.37N, P<0.05) and elasticity (2.81mm±0.07mm, P<0.05). In addition, the storage modulus of A. pernyi pupae flour gel was significantly positively correlated with the solubility (R=0.92) of proteins (P<0.05), but negatively correlated with the proteins coagulate rate (R=-0.52) and surface hydrophobicity (R=-0.77) (P<0.05). At pH 9, the protein solubility was the highest (62.13%±0.63%, P<0.05), and the surface hydrophobicity was the lowest (70.06μg±9.32μg, P<0.05). More small-size thermal aggregates were formed and the gel matrix was enhanced at pH 9. At pH 5, the protein solubility was the lowest (28.96%±1.13%, P<0.05), and the surface hydrophobicity was the highest (195.66μg±1.30μg, P<0.05), which promoted the formation of more large-size thermal aggregates and disorderly stacking, weakening the gel matrix. The purpose of this study was to control the thermal aggregation behavior of protein in A. pernyi pupae flour by adjusting the pH value, and then the gel with ideal texture and water retention could be obtained.