The invention provides an organic compound fertilizer containing agricultural waste and a preparation method thereof, belonging to the technical field of resource utilization of agricultural waste. The organic compound fertilizer containing agricultural waste is prepared from the following raw materials: pretreated agricultural waste, humic acid, alginic acid, trichoderma viride, glucose, agar, microbial powder, wheat bran, pretreated kitchen waste, zeolite powder, magnesium chloride, ferrous sulfate, Baomu bacteria and saccharomycetes. According to the organic compound fertilizer containing the agricultural waste, resource waste and harm to the environment caused by incineration of the agricultural waste are avoided; sustainable application of the agricultural waste is guaranteed; the organic compound fertilizer is balanced in nutrient supply, realizes long-acting slow release and improves the nutrient absorption and utilization rate of crops; and therefore, crop growth is promoted, nutrient metabolism is enhanced, a fertilizer utilization rate is increased, crop yield and quality are improved, soil is fertilized, and benign ecological cycle of soil is promoted.