Pinellia ternata diseases constitute a significant impediment to the industrial development of Pinellia ternata. This research aims to screen and identify excellent strains of beneficial microorganisms resistant to Pinellia ternata, with the ultimate goal of formulating them into microbial fertilizers and exploring their effects on promoting plant growth and disease resistance. Nine strains exhibiting antagonistic effects against various pathogens of Pinellia ternata, including Fusarium oxysporum, Aspergillus, Fusarium, Phytophthora capsici and Fusarium solani, were isolated and screened from the rhizospheric soil of Pinellia ternata. Through the screening and identification of functional bacterial strains, along with the analysis of their determination of their antibacterial capabilities and the evaluation of the growth-promoting and disease control effects of their biological organic fertilizer on Pinellia ternata, the results indicate that strain 21-2 exhibited the most effective antibacterial activity. Upon identification, it was confirmed to be Paenibacillus polymyxa. Strain 21-2 demonstrates notable inhibitory effects against five common pathogens of Pinellia ternata and significantly promotes the germination of Pinellia ternata seeds. The suspension of strain 21-2 exhibits a disease control efficacy of 43.83% against Pinellia ternata diseases, leading to significant improvements in plant height, fresh weight, tuberous bulb, and chlorophyll content, among other growth indicators. The bio-organic fertilizer, comprised of Paenibacillus polymyxa 21-2, straw-derived biochar, and organic fertilizer from chicken manure, exhibits a disease control efficacy of 61.90% against Pinellia ternata diseases, showcasing promising prospects and developmental potential for practical applications.