Strobilurins and anilinopyrimidine fungicides are characterized by high acute toxicity or strong water solubility, which easily pose risks to aquatic environments. In this work, we found that the formulation of tubular g-C3N4 significantly enhanced the adsorption of C3N4/MoS2 compared to other composite morphologies. Notably, the adsorption efficiency of azoxystrobin was enhanced by 203% to 381%, while that for picoxystrobin showed an improvement of 162–186%. To explore the adsorption mechanisms, the adsorption kinetics and isotherms for azoxystrobin and pyrimethanil were thoroughly examined, respectively. The adsorption kinetics followed a pseudo 2nd order kinetics model indicated that 2% C3N4/MoS2 had a chemical adsorption effect on azoxystrobin and pyrimethanil. Thermodynamic parameters confirmed that the adsorption processes of azoxystrobin and pyrimethanil were spontaneous, but the former was exothermic while the latter was endothermic.