To address continuous cropping obstacles，optimize fertilization schemes，and improve yield and quality in lotus root cultivation，a study was conducted in 2023 at a four-year continuous cropping field within the 666.7 hm² lotus root base in Anju district，Suining city. Lotus root variety ‘E Lian No. 6’ was used as the test material，with conventional lotus root-specific fertilizer applied at full rate(T1)serving as the control. Six different fertilizer treatments were implemented to investigate the effects of fertilizer formulations on the quality and yield of continuously cropped lotus roots，as well as on the nutrients and microorganisms in the rhizosphere soil.(1)In terms of yield and quality，compared to T1 treatment，the treatment with a 50% reduction in lotus root-specific fertilizer combined with the full amount of traditional Chinese medicine microbial fertilizer(T4)resulted in the best appearance quality and the highest yield，with the fewest blemishes and the smoothest surface，and the yield was 1320 kg，with an increase of 12.5% compared to T1 treatment. This treatment also significantly increased the contents of starch，crude fiber，soluble sugar，and ascorbic acid，while significantly reduced nitrate content. However，when compound fertilizer was used in combination with traditional Chinese medicine microbial fertilizer(T5，T6，T7)treatment，yields decreased by 16.7%，20.1%，and 25.9%，respectively. In the treatment without fertilizer(T2)，yield decreased by 32.1%，but quality was improved with a significant reduction in nitrate content.(2)The soil nitrogen，phosphorus，potassium nutrient content was lowest in the T2 treatment. Compared with the treatment with reduced lotus root-specific fertilizer(T3)，T4 treatment significantly increased soil available nitrogen，phosphorus，potassium nutrients，organic carbon，and organic matter content.(3)Compared with T1 treatment，T3 treatment increased the Shannon and Simpson indices. Adding traditional Chinese medicine microbial fertilizer(T4)further increased the Observed species and Shannon index of fungal communities，indicating enhanced diversity and richness of fungal communities. This treatment also reduced the relative abundance of Fusarium，adjusted the fungal community structure，and lowered the disease rate of lotus roots. This study demonstrated the potential benefits of integrating traditional Chinese medicine microbial fertilizer with reduced chemical fertilizer application in enhancing both the yield and quality of lotus roots，as well as improving soil health and microbial diversity.