The rotation regimes significantly alter soil properties, however, understanding the effect of crop rotation in various crops system was currently limited. The aim of this research was to reveal the variation in crop productivity, soil nutrients, enzyme activities, and bacterial community composition in vegetable-Polygonatum odoratum rotation horticulture. Thus, a 2-year field experiment was carried out under the P.odoratum-P.odoratum rotation (CC) and vegetable-P.odoratum rotation (FC) system through a randomized complete block design comprising of triplicate plots. The results showed that FC promoted most of the beneficial agronomic traits, soil nutrients, enzyme activities, and reducing root rot disease of P.odoratum. High-throughput sequencing revealed a shift in the microbial community groups with high environmental contaminants degradation ability, and a close correlation between increasing microbial diversity and major environmental factors like soil nutrients, enzyme activities under FC cropping system compared with CC. Therefore, crop rotations with vegetable- P.odoratum was recommended in cultivation.