Limited research investigating the impact of pesticides on antibiotic resistance genes (ARGs) and viral community in the gut of wild animals. In this study, we employed metagenomic to investigate the effects of glyphosate and spinetoram on the gut viral communities, ARGs, and their interactions in a key wild pollinator, bumblebees. The results showed that both 2.5 mg/L glyphosate and 2.5 mg/L spinetoram did not significantly alter the alpha-diversity of the ARGs (p > 0.05). However, spinetoram significantly enriched core ARG subtypes, such as Bado_rpoB_RIF, Bbif_ileS_MUP, and CRP, and total abundance of ARGs (p < 0.05). In contrast, glyphosate had no significant impact on ARG subtypes or total abundance (p > 0.05). The mantel test (R = 0.455, p = 0.020) and Procrustes analysis (M-2 = 0.095, p = 0.069) revealed a significant correlation between the bacterial community and ARGs. Although glyphosate and spinetoram had no significant effect on the relative abundance of mobile ARGs (p > 0.05), both significantly altered the alpha diversity (p < 0.05) and compositional structure (one-way PERMANOVA, p = 0.003) of the gut viral communities, with glyphosate increasing the abundance of lytic phages (p < 0.05). Notably, a phage and host relationship network constructed revealed no evidence of phage-mediated ARGs transduction, but five associations between lytic phages and antibiotic-resistant bacteria (ARB) were identified. Furthermore, glyphosate and spinetoram exposure significantly reduced the total relative abundance of these five lytic phages in the viral community (p < 0.001), indicating that phages primarily function in lysing ARBs. These findings suggest that glyphosate may inhibit the enrichment of ARGs by increasing the abundance of lytic phages, while spinetoram may promote the enrichment of total ARGs by affecting the bacterial community.