The functions and sensory properties of fermented dairy products are influenced by numerous factors, including the type of milk, the strain's degree of protein hydrolysis, and the additives of fermented milk. Currently, a large number of studies have demonstrated that the proteolytic ability of probiotics significantly affects the gel properties of fermented milk. However, few studies have examined the effects of probiotics with varying proteolytic abilities on the functions and sensory properties of fermented dairy products from the protein conformation perspective. Therefore, this study screened Lactobacillus helveticus KLDS1.8701 with a high protein hydrolysis rate and Lactobacillus helveticus KLDS1.0633 with a low hydrolysis rate to investigate the effects of varying degrees of protein hydrolysis on the gel properties, sensory properties and protein conformation of fermented milk. The results showed that the fermented milk containing Lactobacillus helveticus KLDS1.0633 with a low protein hydrolysis degree had high WHC, hardness and viscosity, a dense and uniform structure, abundant pores, and good texture and sensory properties. In addition, compared with fermented milk with high protein hydrolysis, low protein hydrolysis also increased the content of disulfide bonds, low surface hydrophobicity, and more hydrophilic structures such as a-helix. This study explains the impact of differences in protein hydrolysis degree among strains on fermented milk from a new perspective of protein secondary and tertiary conformations, which provides new insights for selecting suitable strains to produce fermented milk with better taste and nutrition.