With the advent of the global energy crisis, the use of sustainable green energy has become more and more widespread and the utilization rate of photovoltaic industry in high-altitude desert areas is getting higher and higher. This article mainly studies the intelligent control system in desert area based on photovoltaic microgrid power supply. The system uses shielded twisted pair to transmit signals, and electrostatic interference and electromagnetic induction interference are effectively suppressed. After ensuring that the encoder feedback is correct and the motor movement direction is consistent with the command direction and the safety of the movement stroke, the PID parameters of the motor are tuned in PAMCturningpro. For the performance test of this system, the design and implementation of the test plan should be carried out according to the concurrent support target and response time target proposed in the performance analysis of the system. Concurrent users use the LoadRunner tool to create the customer test machine to simulate the concurrent access and operation of the system. In each iteration process, the test results are recorded in the same way as the benchmark test and finally the system can still achieve the expected performance when the actual concurrency reaches the limit of 5007. The results show that the intelligent control system in this paper has the advantages of low cost, convenient operation, perfect function, high precision, stable and reliable operation, etc. and has good practical value.