Objective The aim was to investigate the effects of different crop rotations with celery on improving soil micro-ecological environments, and to identify suitable rotation combinations for alleviating celery monoculture problems.

Methods A field experiment was conducted in Xiji County, Guyuan City, using continuous celery cultivation (SSS) as the control, and two rotation treatments were established: pepper-celery (PRS) and green onion-celery (GRS). High-throughput sequencing was used to analyze soil microbial community structure and diversity, combined with measurements of soil physicochemical properties and enzyme activities, to systematically evaluate the comprehensive impacts of different treatments on soil micro-ecology.

Results Compared with SSS, both PRS and GRS significantly reduced disease incidence and increased yield, with no significant difference between the two treatments in terms of disease rate or yield. Both PRS and GRS significantly decreased soil pH by 3.04% and 4.67%, respectively, while increasing total nitrogen, available phosphorus, and organic matter content. Additionally, urease and sucrase activities were significantly enhanced under PRS and GRS: by 4.55% and 3.41% in PRS, and by 8.85% and 7.95% in GRS, respectively. Microbial community analysis revealed that both PRS and GRS increased bacterial and fungal diversity indices, with significant differences in community structures among treatments. Both treatments elevated the abundance of Lysobacter and Aeromicrobium; additionally, PRS significantly increased beneficial bacteria such as Blastococcus and Gemmatimonas. Regarding fungi, PRS and GRS both significantly reduced Gibberella abundance and increased Plectosphaerella and Alternaria abundance, although Fusarium was significantly enriched in GRS. Mantel test and redundancy analysis indicated that soil pH, available potassium, and sucrase activity were key factors influencing bacterial and fungal community structures, with different genera showing specific responses to environmental factors. PLS-PM analysis showed that bacterial communities (λ = 0.901, P < 0.05) and soil enzyme activities (λ = 0.979, P < 0.01) were the dominant factors promoting celery yield increase.

Conclusion The pepper-celery rotation system demonstrated superior overall performance in reducing diseases, increasing yield, improving soil conditions, and optimizing soil microbial community structure, so this system is an optimal rotation model for sustainable celery production in Xiji, Ningxia.