A high reliability wave glider control system comprises a main control computer, a standby computer, a switch module and peripheral equipment, and belongs to the wave glider control field; the main control computer and the standby computer can communicate; the control system has a main control computer processing mode and a standby computer processing mode; the standby computer can be automatically switched according to the conditions that whether the main control computer can normally work or not; the control system also has an integrated weather station GPS positional information fault diagnosis and substitution function, and the present control computer can realize automatic diagnosis and substitution according to the integrated weather station GPS speed information. The high reliability wave glider control system is high in reliability, simple in structure, easy to develop, can effectively improve the wave glider life vitality, and can reduce the missing and loss connection risks thereof.