The coordinate system for smartphones' built-in acceleration sensor is fixed on the equipment itself, the data collected by the smartphone is constantly drifting due to the change of smartphone's posture. Affected by this, even the same movement process, the acceleration is difficult to keep consistent with the previous one. To solve this problem, the acceleration was mapped from smartphone to inertial coordinate system by using space coordinate transformation algorithm, to ensure that the sensor data can accurately reflect actual motion state no matter in what gesture the smartphone is. To verify the effectiveness of this method, a new method for online acquiring and real-time processing smartphone's sensor data was designed. With this method, the feasibilities of direction cosine algorithm and quaternion algorithm were tested in rotation experiments. Then, the performance of quaternion algorithm was further tested in pedometer experiments. The experimental results show that the direction cosine algorithm fails to achieve comprehensive coordinate transformation due to the measurement range limit; while the quaternion algorithm based on rotation vector sensor data can achieve full conversion, and the recognition rate of gait using transformed acceleration is over 95%, which can accurately reflect the actual state of motion.