Abstract: Four pine forests (6-10, 11-15, 16-20 and 31-40 year-old) located in the Cangshan Mountain and Erhai Lake National Reserve and seven pine forests (1-5, 6-10, 11-15, 16-20, 21-30, 31-40 and more than 50 year-old) located in the non-protective area near the national reserve were selected. Three replications of each forest was set and a total of 33 sites were investigated. At each site, we quantified six habitat variables (species richness, abundance and percentage of grasses and shrubs coverage respectively at the bottom layer of forests) within randomly determined 5 m×5 m areas. One hundred cages were set in five lines at each site to trap small mammals, whose species and numbers were recorded. Dominance of Dremomys pernyi and Callosciurus erythraeus in small mammal communities, time niche breadth and time niche overlap between the two small mammals were calculated respectively. Step-wise regression was used to analyze relationship between small mammals and habitat factors. Our results indicated that D. pernyi occurred earlier than C. erythraeus in protective pine forests. D. pernyi was captured in 6-10 year-old forest initially, and C. erythraeus was captured in 16-20 year-old forest initially. D. pernyi and C. erythraeus were captured in the 31-40 and 21-30 year-old forests initially in the non-protective area, respectively. Populations of D. pernyi and C. erythraeus in the 31-40 year-old protective forests were 3 and 3.75 times of those in the same-aged non-protective forests, respectively. Shrubs significantly influenced populations of the two small mammals. Populations of Dremomys pernyi was positively correlated with density of shrubs; populations of C. erythraeus was positively correlated with coverage of shrubs, and negatively correlated with coverage of grasses. D. pernyi and C. erythraeus were important for pine forests to scatter pine seeds. Human activities in the non-protective pine forests decreased the vegetation heterogeneity at the bottom layer of pine forests, postponed the occurrence of D. pernyi and C. erythraeus, and decreased populations of the two small mammals.