The invention relates to a chitosan sustained release microsphere fertilizer loaded with thiophanate-methyl for tomatoes, which is characterized by being prepared from the following raw materials: chitin, sodium hydroxide, thiophanate-methyl, propiconazole, acetone, sodium dodecyl benzene sulfonate, acetic acid, polyethylene glycol diglycidyl ether, cyclohexane, epoxy chloropropane, glutaraldehyde, petroleum ether, isopropyl alcohol, lithopone, coal ash, attapulgite, plant ash, potassium pyrophosphate, sodium alga acid, hexamethylene diisocyanate, triethylene diamine, human and animal excreta, urea, monocalcium phosphate, zinc sulfate, and appropriate amount of water. The fertilizer prepared by the invention integrates increased production, high efficiency, long effect, quality improvement, and soil improvement into a whole, and has the advantages of low cost, simple process, no residue, no pollution, labor and time saving when being applied, and the like.