The invention relates to a vehicle compartment with a waterproof structure capable of preventing water from infiltrating into the vehicle compartment and a manufacturing method thereof. Specific to the defect that when a sealant on a contact surface of a wrap angle and a top plate of the traditional vehicle compartment is aged, water accumulated at the top of the vehicle compartment infiltrates into the vehicle compartment and the interior of a wall of the vehicle compartment, and steel materials inside the compartment body are rusted away, the invention provides the vehicle compartment with the waterproof structure capable of preventing water accumulated at the top of the vehicle compartment from infiltrating into the vehicle compartment and the interior of the wall of the vehicle compartment when the sealant on the contact surface of the wrap angle and the top plate is aged and the manufacturing method of the vehicle. The vehicle compartment with the waterproof structure and the manufacturing method, provided by the invention, adopt the technical scheme that diversion plates are arranged below peripheral edges of the top plate of the vehicle compartment; water troughs are arranged on the diversion plates; upper drain outlets are arranged below four corners of the top plate, and notches of the water troughs on the diversion plates are fixed at the upper drain outlets; lower water trough plates are arranged at the part where two adjacent side panels are crossed, the upper ends of the lower water trough plates are matched with the upper drain outlets arranged below the four corners of the top plate, and the lower ends of the lower water trough plates are matched with lower drain outlets arranged below four corners of a bottom plate.