Focusing on the first domestic developed airborne three line CCD camera (GFXJ), it is carried out that the innovative investigation work on GNSS lever arms and IMU boresight misalignment calibration of GFXJ camera. Firstly, a brief introduction is given on the imaging properties of GFXJ camera. Then, the GNSS level arms calibration model and IMU boresight misalignment calibration model are built for GFXJ camera after detailed investigation. Meanwhile, the iterative two-step calibration scheme is put forward for the GNSS level arms and IMU boresight misalignment calibration of GFXJ camera. Finally, multiple sets of flight data are captured under the support of the national Songshan remote sensing comprehensive testfield. Through the block adjustment and calibration experiments of these sets of imaging data, it verifies the correctness and the efficiency of proposed GNSS lever arms calibration model and IMU boresight misalignment calibration model, and also demonstrates the reliability and practicability of the iterative two-step calibration scheme for GFXJ camera. The proposed calibration scheme can significantly enhance the geometric positioning accuracy of GFXJ camera. Using the GNSS level arms and the IMU boresight misalignment calibration values, the uncontrolled positioning accuracy of GFXJ camera can be significantly improved. Aided with several control points for re-block adjustment, the planar positioning accuracy of GFXJ camera can fulfill the accuracy requirements of 1:1000 scale mapping, but there still exists a little gap between its height positioning accuracy and the 1:1000 scale mapping requirements. The camera is still in the calibration flight stage, its geometric performance can be further improved after product approval. Moreover, the GNSS lever arms calibration model, the IMU boresight misalignment calibration model, and the iterative two-step calibration scheme put forward in the paper can be applied to calibration work for other airborne CCD cameras.