In this paper, we propose an Extended Kalman Filtering with phase noise reconstruction (EKF-PC) scheme to enhance the carrier recovery capability for probabilistic shaping of coherent optical communication systems with various shaping factors. We first investigate the weights of the shaping factor and the noise rejection window length of EKF-PC for PS-64QAM at a fixed signal-to-noise ratio (SNR). After that, we jointly optimize the shaping factor and the noise rejection window length to obtain the maximum achievable information rate at a variety of SNRs. Then, we numerically analyze the carrier recovery performance of the EKF-PC for different linewidths and SF conditions. Finally, we conduct simulation experiments to compare EKF-PC, PCPE, and other currently available Kalman CPE algorithms with the SFs of 0.02, 0.025, 0.03, and 0.035 under back-to-back (B2B) scenarios. The experimental results show that EKF-PC obtains an average SNR improvement of 0.13–0.5 dB compared to PCPE and an average performance improvement of 0.5–1 dB compared to other Kalman algorithms.