The flight performance evaluation of navigation system is very significant because the reliability of navigation data directly affect the safety of aircraft. Especially, the high-level navigation system such as DGPS/INS, need more precise flight performance evaluation method. The performance analysis is evaluated by comparing between the navigation system in aircraft and reference trajectory which is more precise than navigation system in aircraft. In order to verify DGPS/INS performance of m-level, the GPS receiver, which is capable post-processed Carrier-phase Differential GPS(CDGPS) method of cm-level, have to be used as reference system. The DGPS/INS is estimated the Center of Gravity (CG) point of aircraft to offer precise performance while the reference system is output the position of GPS antenna which is mounted on the outside of aircraft. Therefore, in order to more precise performance evaluation, it needs to compensate the lever arm and coordinates transformation. This paper use quaternion and Direct Cosine Matrix(DCM) methods as coordinate transformation matrix in lever arm compensation of CDGPS reference trajectory. And it compares NED errors of DCM and quaternion transformation in lever arm of reference trajectory via DGPS/INS result.