The invention discloses a differential type magnetic simulator for a small satellite and a control method thereof, and belongs to a magnetic simulator and a control method thereof. The differential type magnetic simulator comprises a control computer, a gauss meter, a unipolarity constant flow source and a triaxial magnetic coil; wherein, the gauss meter comprises a gauss meter probe and a gauss meter processor; the unipolarity constant flow source comprises X axle main constant flow source, X axle auxiliary constant flow source, Y axle main constant flow source, Y axle auxiliary constant flow source, Z axle main constant flow source and Z axle auxiliary constant flow source; the triaxial magnetic coil comprises X axle main coil, X axle auxiliary coil, Y axle main coil, Y axle auxiliary coil, Z axle main coil and Z axle auxiliary coil. In the control method, the triaxial energizing current is calculated by using the target magnetic field value and a coil constant matrix directly when the differential type magnetic simulator works in an open-loop working manner; when the differential type magnetic simulator works in a close-loop working manner, the real-time output of the gauss meter is used for adjusting the energizing current slightly. The invention has the advantages of simple structure and high detection precision.