With the boom expansion of chemical industry, antibiotic-contaminated organic fertilizer and irrigation may be applied to agroecosystems that have been exposed to fungicides. However, it is not clear how the co-occurrence of fungicides and antibiotics will affect microorganisms and resistance genes. In this study, we determined cyazofamid (CZF) of soil and earthworm tissue with ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) and the change of bacterial community structures and antibiotics-resistance genes (ARGs) was analyzed by 16S rRNA gene sequencing and high-throughput quantitative PCR, respectively. After co-occurrence of fungicide and antibiotic, we did not observe significant differences in environmental behavior, but joint pollution was more toxic. Physiological indicators showed that growth process and earthworm survival rate were harmed after co-occurrence of fungicides and antibiotics. Bacterial community structure was significantly perturbed and enriched specific, such as Acinetobacter, Sphingobacterium, Comamonas, Rhodococcus and Sporosarcina. Moreover, the prevalence of fungicides and antibiotic exerted a selective pressure for ARGs in the environment, which were in high risk of being horizontally transferred to other bacteria and pathogens through mobile genetic elements (MGEs) such as insertional, transposons, and plasmids. Stress-tolerant contributing and the potential pathogenicity species (e.g., Rhodocyclaceae) may also harbor microbial functions ko00791(Atrazine degradation), and ko00980 (Metabolism of xenobiotics by cytochrome P450). Statistically significant good correlation between MEGs and ARGs was also found. Our novel findings extend the fundamental information that sample types, pollutants, bacteria, functions, and MGEs are critical factors in shaping bacterial communities and antibiotic resistances.