A system structure with a fan module. The system structure has a housing and a fan module. The housing has a substrate with the fan module detachably installed thereon. The substrate has a plurality of guide ports, several first positioning portions and a second positioning portion. The fan module has a body, two plates and a fan unit. Each plate is detachably disposed on the body and provided with several positioning portions. When the fan module is attached to the substrate of the housing, the third positioning portions of the fan module are fixed by the first positioning portions of the substrate, and the fourth positioning portion of the fan module fits into the second positioning portion of the substrate.