In an integrated location system, the establishment of mutual attitude relationships between different subsystems is accomplished by the alignment processing. When the inertial component is used for positioning, the attitude and heading reference system(AHRS) is generally based on geographic coordinate system(E-N-U) as the navigation coordinate system. However, during indoor navigation task, the navigation coordinate system is generally based on the users′ requirement such as marked points or workpiece coordinate system. In this paper a new alignment method based on direction cosine matrix was proposed for the integrated positioning system of indoor mobile object. The transformation between geographic coordinate system and external reference coordinate system can be achieved by the method.Then coordinate system of laser tracker became navigation reference and real-time and precise transformation between different coordinate systems can be realized by this new alignment method.Experimental results show that the measured RMS errors for attitude angles after transformation are less than 0.25° while the AHRS is in arbitrary position and orientation.