This paper describes a calibration procedure for compensating for misalignments associated with a triaxial magnetometer onboard a spinning projectile. The geometric misalignment of sensors from chosen axes will create errors in the readout. These misalignments can be compensated in an onboard calibration process, and a calibration method without external attitude aids is proposed which consists of two steps. The first step is to eliminate the inherent instrumentation errors which generally called scalar calibration. The second step introduces a simple and useful sensor axis pointing alignment method. In the second step, misalignments can be quantified using perturbation theory that assumes small angular offsets of the sensors, and this is a reasonable approximation. Then the magnetic vector can be deduced and obtained with relatively high accuracy, which is essential for such as geomagnetic navigation application. Simulation results are presented and discussed, supporting the availability of the presented approach to the spinning scenarios.