A method of reconfigurable parallel information processing in GNC was proposed for conflicting issues between high calculation performance and low power consumption in information processing of cubesats. An architecture of tightly coupled reconfigurable parallel processing was adopted in the method and complex algorithms which require many iterations and are not suitable for CPU operations in GNC information processing were achieved by dynamically partial reconfigurable unit of the hardware circuit (DPR). A multi-core parallel reconfigurable resource scheduling algorithm based on mutex was adopted in the method and optimized hardware acceleration of the software algorithms was completed through multi-core CPU parallel calls by DPR unit. The experimental results indicate that real-time information processing of GNC is effectively achieved in cubesats and reduces power consumption up to 50%. The method can be widely used in the field of imformation processing for resource-constrained satellites and possesses a great application prospect.