A dynamic calibration method was proposed to determine the relative orientation of the axes of the strapdown inertial navigation system (SINS) and the CCD star sensors (CSS) for shipboard SINS/CSS system at the rigid and flexure installation conditions. Specifically, the Kalman filtering method is utilized to estimate the SINS attitude error and the CSS installation error, in which the observation function is founded by using the attitude data separately measured by CSS and SINS, and the state function is constructed by using SINS navigation error functions. To validate the proposed calibration method, the simulation experiments are studied by using the actual navigation data and ship flexure data measured by Yuanwang Ⅲ TT&C ship. Results show that the calibration can achieve a high accuracy when the CSS and the SINS are rigidly installed together, while the calibration error will increase when the CSS and the SINS are separately installed at different locations for ship flexure influence.