Silviculture of appropriate tree species can improve soil properties, subsequently ameliorating the productivity and ecological functions. However, it is not clear about the differences in the effects of tree species on soil properties in secondary forest ecosystems. In this study, four stands of 60–70 years secondary forests were chosen. Eight replicate individuals of five common native tree species: Acer mono, Quercus mongolica, Juglans mandschurica, Fraxinus rhynchophylla, and Fraxinus mandschurica were selected in each stand to test the effects of tree species on soil properties in a typical temperate secondary forest ecosystem in Northeast China. Forest floor, soil at three depths (0–10, 10–20 and 20–40 cm) were compared among five tree species. Our findings showed significant differences in soil mineral nitrogen (N) (i.e. NH4+-N and NO3–-N) and available phosphorus (P), microbial biomass C (MBC), microbial biomass N (MBN) and enzyme activities depending on the tree species. At 0–10 cm soil depth, F. mandschurica soils exhibited 18–28% higher mineral N than those A. mono, F. rhynchophylla, and Q. mongolica, 24–38% higher available P than Q. mongolica and F. rhynchophylla. Similarly, F. mandschurica soils showed 64–66% higher MBC and MBN than Q. mongolica, and 41–133% higher β-glucosidase enzyme activity than J. mandshurica, F. rhynchophylla, and Q. mongolica. At 10–20 cm soil depth, F. mandschurica exhibited higher soil mineral N and available P concentrations, MBC, enzyme activities of phenol oxidase, exoglucanase, and β-glucosidase than the other tree species. At 20–40 cm soil depth, there were no difference in soil mineral N and available P, MBC, MBN, and enzyme activities among five tree species. No differences were observed between the tree species in the C, N, and C/N ratio of forest floor; however, the C/N ratio of fine roots was lower for F. mandschurica than for Q. mongolica. Significant correlations were established between C/N ratio of fine roots and soil mineral N and available P, MBC and MBN, and phenol oxidase. This suggests that the high quality of F. mandschurica fine roots improved soil chemical and microbial properties. Nevertheless, these native tree species exhibited improving soil chemical and microbial properties, compared to larch plantation soils in secondary forest ecosystems. Therefore, we suggest that introduction of F. mandschurica followed by that of A. mono and J. mandshurica, and then Q. mongolica and F. rhynchophylla into larch plantations should be considered for restoring the degraded soils in plantations.