Under global climate change, biodiversity is decreasing rapidly due to deforestation and habitat fragmentation, which has serious consequences for ecosystem functioning. In recent years, the relationship between biodiversity and ecosystem functioning has been a core research area in ecology. Previous researchers have paid great attention to the relationship between biodiversity and individual ecosystem functioning, and seldom consider multiple functions (multifunctionlity), especially in forest ecosystems. Here, based on survey data from 94 plots of Pinus yunnanensis in a natural secondary forest, we selected variables related to ecosystem functioning: woody plant biomass, soil organic carbon, plant nitrogen, plant phosphorus, soil total nitrogen, soil hydrolyzable nitrogen, soil total phosphorus, and soil available phosphorus. We used an averaging approach, single threshold approach, and multiple threshold approach to evaluate the effects of species richness on ecosystem multifunctionality and impacting factors. Results showed that the relationship between species richness and ecosystem multifunctionality was stronger than that of individual ecosystem functioning. Species richness had a significant positive effect on multifunctionality within thresholds ranging from 3% to 88%. When using a moderate threshold (54%), species richness had the strongest positive effect, and the percentage of maximum possible species richness was 53.53%. Path analysis of a structural equation model showed that species richness had the strongest (positive) effect on multifunctionality in the Pinus yunnanensis natural secondary forest. Mean annual temperature, mean annual precipitation, and soil pH had insignificant effects on multifunctionality, but indirect effects via influences on species richness. Species richness may be of primary importance when considering ecosystem multifunctionality. Increasing species numbers may not always lead to the optimal state of all functions. Increasing species numbers had the strongest effects on multifunctionality, but only once multifunctionality reached moderate levels.