Carrier phase difference measurements for the same satellite navigation signal at each antenna array elements can be used to solve its direction of arrival (DOA). However, traditional tracking algorithms can only adopt separate tracking loops for each separate antenna element when moderate interference is present; these algorithms cannot obtain precise measurements and frequently become lose of lock. Aim to solve these problems, a joint carrier tracking algorithm which decomposed each element′s carrier phase to the common average part and the low dynamic residual part was proposed. For the average carrier phase, as it is commonly shared by each array element, its tracking accuracy can be improved by combining all the observation values of the whole array elements. For the residual carrier phase, its tracking accuracy can be improved by reducing the loop noise bandwidth. Theoretical analysis and numerical simulation show that the algorithm can significantly improve the measurement accuracy of carrier phase difference between elements needed by DOA estimation and tracking sensitivity. The tracking sensitivity of a 4 element antenna array with typical application conditions improves 4dB and the carrier phase difference measurement accuracy of it increases 3 times under the same carrier noise ratio.