In order to investigate the effects of intercropping Centrosema pubescens or Grona styracifolia on soil physicochemical properties, microbial community structure and diversity in the litchi orchard, soil samples from 0 to 40 cm depth between litchi tree rows were collected under intercropping with either C. pubescens or G. styracifolia. Physicochemical factors such as soil organic matter, total nitrogen, total phosphorus, total potassium, nitrate nitrogen, ammonium nitrogen, available phosphorus, available potassium and pH were measured. In addition, Illumina NovaSeq sequencing platform was used for 16S amplicon sequencing to analyze the microbial communities in the soil under intercropping with C. pubescens or G. styracifolia in the litchi orchard. The results showed that the nutrient content in the 0-20 cm soil layer was generally higher than that in the 20-40 cm soil layer. In the 0-20 cm soil layer, the C. pubescens intercropping treatment increased soil organic matter by 7.06%, total nitrogen by 8.70%, and ammonium nitrogen by 103.29%, compared to the control. In the intercropping treatment with G. styracifolia, soil ammonium nitrogen increased by 69.41%, nitrate nitrogen increased by 32.48%, available phosphorus increased by 112.78%, and available potassium increased by 9.44%, compared to the control. In the 20-40 cm soil layer, the C. pubescens intercropping treatment increased soil ammonium nitrogen by 114.58%, but decreased available potassium by 48.07%, compared to the control. In the intercropping treatment with G. styracifolia, soil nitrate nitrogen decreased by 15.07%, while available phosphorus increased by 105.43% and available potassium increased by 32.60%, compared to the control. In terms of microbial diversity, the indices in the 0-20 cm soil layer were generally higher than those in the 20-40 cm soil layer. In the 0-20 cm soil layer, the ACE index and Chao1 index in the C. pubescens intercropping treatment were decreased by 7.65% and 7.68%, respectively, compared to the control. In the 20-40 cm soil layer, the ACE index and Chao1 index in the intercropping treatment with G. styracifolia were increased by 6.93% and 6.74%, respectively, compared to the control. In terms of soil microbial community structure, the dominant phyla in all soil samples were Acidobacteria, Chloroflexi, Proteobacteria, Firmicutes, and Actinobacteria, while the dominant genera were Gp2, Gp13, Bryobacter, Candidatus Solibacter and Bathyarchaeia within the Acidobacteria phylum. After intercropping, the relative abundance of Thaumarchaeota, Nitrospirae, Verrucomicrobia, Gp2, Gp13 and Bryobacter increased. Redundancy analysis indicated that pH, total potassium, total phosphorus, and available potassium were the main physicochemical factors affecting soil microbial community structure. In summary, the results of this study would provide a theoretical basis for intercropping with C. pubescens or G. styracifolia in litchi orchards.