The invention provides a pyraclostrobin-difenoconazole microcapsule suspension agent and a preparation method thereof, wherein the pyraclostrobin-difenoconazole microcapsule suspension agent comprises, by mass, 1-20% of pyraclostrobin, 1-40% of difenoconazole, 6-10% of a microcapsule wall material, 15-20% of a microcapsule core solvent, 1-5% of an emulsifier, 0.1-1% of a thickener, 3-5% of a dispersant, 1-5% of an anti-freezing agent, 0.1-0.5% of a preservative, 1-3% of a pH value regulator, 0.1-1% of a curing agent, and the balance of water. According to the present invention, by successfullycompounding pyraclostrobin and difenoconazole, the synergistic effect is provided, the prevention and control effect is significantly improved, the pesticide consumption is reduced, and the environmental pollution and the pesticide residue are effectively reduced; and the pyraclostrobin-difenoconazole microcapsule suspension agent has advantages of good quick-acting property, long lasting time, environmental protection and good market potential.