In order to suppress the geometrical artifacts caused by random jitter in ray source scanning, and to achieve flexible ray source scanning trajectory and meet the requirements of task-driven scanning imaging, a method of free trajectory cone-beam computed tomography (CBCT) reconstruction is proposed in this paper. This method proposed a geometric calibration method of two-dimensional plane. Based on this method, the geometric calibration phantom and the imaging object could be simultaneously imaged. Then, the geometric parameters could be obtained by online calibration method, and then combined with the geometric parameters, the alternating direction multiplier method (ADMM) was used for image iterative reconstruction. Experimental results showed that this method obtained high quality reconstruction image with high contrast and clear feature edge. The root mean square errors (RMSE) of the simulation results were rather small, and the structural similarity (SSIM) values were all above 0.99. The experimental results showed that it had lower image information entropy (IE) and higher contrast noise ratio (CNR). This method provides some practical value for CBCT to realize trajectory freedom and obtain high quality reconstructed image.