A window-split frequency domain Kalman scheme is proposed in this paper for the equalization of large polarization mode dispersion (PMD) and ultra-fast rotation of state-of-polarization (RSOP) which is an extreme environment due to the Kerr effect and the Faraday effect under the lightning strike near the fiber cables. In order to carry out the proposed Kalman scheme, we give a simplified and equivalent fiber channel model as a replacement for the general model of the polarization effect of the co-existence of PMD and RSOP. With this fiber channel model, we can conduct compensation for PMD in the frequency domain and tracking RSOP in time domain. A half analytical and half empirical theory for the initialization of the process and measurement noise covariance is also presented in theory and verified by the numerical simulation. The performance of the proposed Kalman scheme is checked in the 28Gbaud PDM-QPSK coherent system built on both simulation and experiment platforms. The simulation and experiment results confirm that compared with the generally used constant modulus algorithm (CMA), the proposed scheme provides excellent performance and stability to cope with large range DGD from 20ps to 200ps and RSOP from 200krad/s to 2Mrad/s, with less computational complexity.