Being capable of directly utilizing solar thermal energy, the solar membrane distillation desalination system (SMDDS) has evolved as a promising green technology for alleviating the water resource problem. This paper reports the experimental and simulation study of a SMDDS which utilizes the air gap type membrane distillation. A laboratory system with automatic control function was established. A control scheme for fully automatic operation was designed using the PI (proportional–integral) control algorithm, which is robust and commonly employed by industries. The control structure adopted PI temperature control for the solar thermal and the membrane distillation subsystems. A dynamic mathematical model including the control algorithm for the overall system was developed, built on Aspen Custom Modeler® platform, and verified by the experimental results. The optimization analysis using the model reveals the operation strategy for maximum water production. Because of the unpredictable solar irradiation, the corresponding optimal dynamic operation cannot be pre-determined and implemented during system operation. However, the proposed PI control scheme could provide a fairly good level of performance, for example up to about 80% of the maximum water production for sunny day operation.