[Objective] This study aimed to explore the effects of Scutellaria organic fertilizer on the basic characteristics and microbial community diversity and function of soil under continuous cropping of potato can provide theoretical references for the resource utilization of Scutellaria residue and the improvement of continuous potato cropping soils. [Methods] Using the residue of the medicinal herb Scutellaria baicalensis and sheep manure （with a mass ratio of 1∶3）as the base materials，three organic fertilizer systems（labeled as T1，T2，and T3 in sequence） were prepared by fermentation after adding 3%， 5%， and 10% functional microbial agents respectively. The corresponding treatments after the organic fertilizer was applied to the soil were labeled as F1， F2，and F3，respectively. The effects of the three Scutellaria residue organic fertilizer systems on soil chemical properties，bacterial diversity and function of continuous potato cropping fields were analyzed with the in-situ control trial. [Results] 1）Compared with the control group，all three Scutellaria residue organic fertilizer systems significantly increased the available phosphorus and available potassium contents of the soil at the maturity stage， with increases of 8.12~12.00 mg/kg and 65.63~88.36 mg/kg，respectively. 2）The total population of bacterial flora in potato surface soil was increased by 60.96% and 23.19% in F1 and F2 treatments，and enriched with beneficial genera such as Sphingomonas，Pseudoxanthomonas，and Flavobacterium. 3）LEfSe analysis showed that the application of Scutellaria residue organic fertilizers suppressed the absolute abundance of pathogenic bacteria such as Pectobacterium in the soil，and enriched more beneficial bacterial communities with significantly high absolute abundance that promote soil element cycling. 4）The three kinds of Scutellaria residue organic fertilizer systems altered the function of soil bacterial mediated carbon and nitrogen cycling，and increased the organic matter decomposition potential of soil flora and soil nitrogen availability. [Conclusion] The application of Scutellaria residue organic fertilizer can improve soil available phosphorus and potassium nutrient content，the abundance of beneficial bacterial genera，and bacterial functional activity. The system T1 is the best Scutellaria residue organic fertilizer system.