The study aims to investigate the mechanisms of different bio-fertilizers on soil environment, rhizosphere microbial communities, growth indicators and yield of continuously cropping celery, providing a theoretical basis for alleviating continuous cropping obstacles. A field experiment of fertilizer efficiency was conducted in a greenhouse with celery continuously cropped for three years. Four treatments were established, including self-made cow dung bio-fertilizer (NF), Chinese herbal residue bio-fertilizer (ZYZ), commercial bio-organic fertilizer (DL), and a blank control (CK). Soil chemical indicators and nutrients were analyzed, rhizosphere microbial communities were characterized, and growth traits and yield were measured to reveal the correlations among these variables. The results showed that ZYZ significantly increased the contents of soil organic matter and available iron, manganese and other trace elements. NF showed a distinct advantage in boosting available zinc. Bacterial communities were significantly driven by pH and organic matter, with ZYZ specifically enriching beneficial bacteria such as Bacillaceae, and NF increasing fungal diversity. Fungal communities were more responsive to available phosphorus and potassium. DL treatment resulted in reduction of bacterial diversity. ZYZ increased the stem diameter and plant height of celery, whereas the yield-increasing effects of NF and ZYZ were both superior to that of DL, with NF increasing yield by 12.01% and ZYZ by 10.50%. Self-made bio-fertilizers alleviate continuous cropping obstacles in celery by activating soil nutrients and reshaping the rhizosphere microbiome. NF performed outstandingly in yield increase, while ZYZ supported better vegetative growth, providing practical insights for developing specialized bio-fertilizers for continuous cropping systems.