The forest ecosystem is an important part of the terrestrial ecosystem carbon sink, and its rate of biomass accumulation influences its carbon sink potential. Therefore, it is particularly important to understand the biomass and productivity of forest ecosystems, and their driving factors, especially in karst areas with a fragile ecological environment. We established a 2 ha plot in karst forest in southwest China, and investigated species composition, community structure, topography and soil nutrients in the years 2007 and 2017. In this analysis, the correlations between tree diversity and each factor were evaluated using a Pearson correlation analysis. In addition, the relationships between soil nutrients and topographies and their effects on productivity and biomass were further evaluated, either directly or indirectly, through species and structural diversity by using a structural equation model (SEM). The results showed that the number of individuals in each species decreased, and productivity was 1.76 Mg ha−1 yr−1, from 2007 to 2017. Species diversity was negatively correlated with biomass and positively correlated with productivity; structural diversity was negatively correlated with biomass and productivity, while structural diversity was negatively correlated with biomass and positively correlated with productivity. In addition, the effects of soil factors on biomass and productivity were significantly different: TN had a significant positive effect on productivity, while all soil factors except total nitrogen (TN) had significant positive effects on biomass. The structural equation results also showed that topographic and soil factors can directly affect productivity; structural diversity has a strong direct negative impact on biomass, while species diversity, structural diversity and biomass have similar direct positive impacts on productivity. Structural diversity was better than species diversity when explaining biomass accumulation. In conclusion, biotic and abiotic factors both influence forest productivity in karst forests in southwest China, and improving species diversity and community structure complexity is of great significance for forest management and productivity promotion. The research further improve the understanding of biomass and productivity in karst forest ecosystems, and their driving factors, which will provide relevant theoretical support for sustainable forest development in southwest karst.