In this paper, a new nonintrusive method of measuring permeate flux for membrane distillation is proposed, based on the law of conservation of energy. Only the surface temperatures at selected regions of a membrane are nonintrusively measured using an infrared camera and they are used to predict permeate flux. Unlike traditional methods, this new method can monitor temperature changes in real time in a nonintrusive way, and it can accurately measure the permeation flux of the membrane with a smaller error. The method is validated with a combination of experiments and computational fluid dynamics (CFD). The results of the simulation provide rich physical details including local heat and mass fluxes, local Nusselt numbers and TPC (Temperature polarization coefficient). This suggests that the permeate-side hydrodynamics play an important role in improving the heat transfer in cross-wise SGMD. The maximum error between the permeate flux measured with the new method and that of the simulation was within 9%. This method provides a guide for the precise evaluation of membrane-distillation performance exactly.