The prevention and control of pests and diseases are becoming increasingly difficult owing to extensive pesticide resistance. The synergistic use of pesticides for disease control is an effective way of slowing pesticide resistance, reducing the number of pesticide applications, and protecting the environment. In this study, a dual-functionalized pesticide nanocapsule delivery system loaded with two active ingredients (AIs)—validamycin and thifluzamide—was developed to prevent and control rice sheath blight; the nanocapsule system was based on a water–oil–water double emulsion method combined with high-pressure homogenization technology. Our results showed that the dual-functionalized pesticide nanocapsules were monodisperse spheres with a mean particle size of ~260 nm and had good storage stability. Compared with commercial formulations, the dual-functionalized pesticide nanocapsules exhibited good foliar spread owing to their small size, which is beneficial for reducing the loss of pesticides on the leaves. The 50% median effect concentration and synergistic ratio against Rhizoctonia solani of the dual-functionalized pesticide nanocapsules and commercial formulation were 0.0082 and 0.0350 μg/mL, and 2.088 and 0.917, respectively. These findings indicate that the bioactivity of the dual-functionalized system was significantly better than that of the commercial formulations and that the dual-functionalized system demonstrated a clear synergistic effect between the two AIs. The system presented here is simple, fast, and capable of dual-pesticide loading with significant synergistic effects. Our findings could help to facilitate the improvement of pesticides efficiency and the slowing of pesticide resistance.