The most suitable growth stage for harvesting L. chinensis while balancing yield and nutritional value has been poorly studied. Moreover, few studies have examined the response of L. chinensis to different organic fertilization strategies and the potential dynamic soil microbial ecological mechanisms. We conducted a two-year field experiment to investigate the impacts of different fertilizers on L. chinensis biomass and quality and the responses of soil microbiomes at three sampling stages. L. chinensis biomass in organic fertilizer (OF) and biofertilizer (BIOF) treatments was significantly (P < 0.05) elevated compared with that in the control (CK: nonamended) at all sampling stages. Significant difference of crude protein among different fertilization regimes was found in flowering and fruiting stages, respectively. Bacterial and fungal H_Shannon and S_Chao1 were positively (P < 0.05) associated with L. chinensis biomass. Three sampling stages were primarily and significantly separated in terms of the soil microbial communities. Besides, CK, OF, and BIOF were also significantly separated within each growth stage. Sampling stages, fertilization regimes and soil properties explained 15.0% and 20.8% of the observed bacterial and fungal community variations, respectively. Mantel test results showed that the soil microbial community compositions had a significant correlation (bacteria, P = 0.019; fungi, P = 0.001) with L. chinensis biomass. Our research provides evidence for the relationships between dynamic responses of soil microbial community and L. chinensis production, which enriches the soil microbial ecology promotion theory and contributes to an important theoretical and scientific basis for extensive guidance of L. chinensis planting process.