The invention discloses compound biochar-based slow-release fertilizer and an application method thereof and mainly relates to the field of biochar-based fertilizer. A preparation method of the compound bio-carbon-based slow-release fertilizer comprises mixing agricultural rice straws and wood shavings, preparing char, adding sodium selenite into the char to obtain biochar, mixing pig manure and chicken manure, carrying out fermentation on the pig manure and chicken manure, carrying out metal passivation treatment to obtain manure-based fertilizer, further fermenting the biochar and the manure-based fertilizer, and adding diatomite into the fermentation product for modification to obtain slow release fertilizer granules. In use, preferably, the slow-release fertilizer granules are applied to the field according to a ratio of 256 kg per mu, and a field moisture capacity measured value is kept in a range of 70% to 80% in the whole growth period. The compound biochar-based slow-release fertilizer can meet the demand of nitrogen and phosphorus in the early stage and the whole period of rice seedling, has sufficient and lasting fertilizer effects, prevents the effects of heavy metals, improves the soil environment, inhibits methylmercury, and can produce high-yield good-quality selenium-rich rice.