The invention relates to a modified starch-PVA-based composite agricultural mulching film and a preparation method thereof. Processing materials of the modified starch-PVA-based composite agricultural mulching film comprise the following components in parts by weight: 80-120 parts of modified starch, 20-30 parts of PVA, 10-15 parts of a plasticizer, 1-2 parts of a binder, 2-3 parts of a cross-linking agent, 1-2 parts of a release agent, 10-18 parts of propolis, 10-15 parts of chitosan, 5-10 parts of organobentonite and 0.6-0.8 part of an antioxidant. The modified starch and the PVA are taken as subject materials and a proper amount of propolis powder and chitosan are added, so that the modified starch-PVA-based composite agricultural mulching film has excellent deodorant and antibacterial properties and has good bearing capacity and barrier property; and the strength and the toughness of the agricultural mulching film are greatly improved. The preparation method is reasonable in process, high in production efficiency, easy in industrial realization, and a product is uniform in quality and good in stability.