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Purpose Plant litter is the main source of soil organic matter, regulating soil microbial community diversity and structure. However, the effects of plant litter traits on soil fungal and bacterial community diversity are still unknown in highly intensive citrus orchards, which represent a special ecosystem that combines the characteristics of farmlands (high input of chemical fertilizers) and natural forests (no tillage and perennial plants). Methods A microcosm experiment was conducted to assess the effects of citrus leaves (C), alfalfa leaves (A), and the mixture of citrus and alfalfa leaves (CA) on soil bacterial and fungal diversity and community structure in citrus soils. High-throughput sequencing was used to investigate the varied patterns of soil microbial community during the leaf litter decomposition process. Results Plant litter addition enhanced soil fungal diversity and increased bacterial diversity in the C and A treatments. Alfalfa litter significantly increased soil fungal diversity, but had no significant effect on bacterial diversity. Citrus leaves decreased soil bacterial diversity, and the mixture (CA) caused an increase in bacterial and fungal diversity when compared to the control (CK). Litter addition also significantly changed soil bacterial and fungal community structure, with changes in fungal community structure being more obvious than those in bacterial community structure. Litter addition mainly changed rare bacteria and fungi with lower relative abundance, while abundant bacteria and fungi showed no obvious changes in response to plant litter decomposition. Conclusions This study highlights that soil microbial diversity is sensitive to plant litter diversity, and different litter traits result in different patterns of bacterial and fungal diversity and community structure in orchards. These results suggest that citrus-derived volatile organic compounds (VOCs) have negative effects on bacterial diversity, and alfalfa leaves improve fungal diversity. The mixture of C and A plays positive roles in both bacterial and fungal diversity. Rare microbes show the most response to leaf litter decomposition, which might play important roles in maintaining soil fertility and health.