The MEMS magnetometer determines the orientation for the MEMS inertial system. Because of the large noise of the MEMS magnetometer and the interference of soft and hard iron outside, the measurement error of the MEMS magnetometer is large. To reduce the effects of the random noises, the MEMS magnetometer arrays are designed in this paper. In our design, thirty-two MEMS magnetometers are welding on a printed circuit board (PCB), which area is 5×5 cm2. The forty general-purpose input-output (GPIO) ports, which are thirty-two data ports and eight clock ports, are used to collect the data of MEMS magnetometers. Then, averaging the thirty-two measurements of the MEMS magnetometers, the random noises of the measurements of the MEMS magnetometers can be reduced. Based on the averaging operation for the collected sensors’ data, a unified measurement model for the MEMS magnetometer arrays is constructed. Using the unified measurement model, an adaptive Kalman filter is developed to estimate the unknown parameters. To validate the performance of the MEMS magnetometer arrays, the simulation and experimental tests are designed. The test results show that, comparing with the single MEMS magnetometer, the random noises of the MEMS magnetometer arrays are reduced effectively.