Polarization mode dispersion (PMD) has been the major limiting factor for long-haul high-speed optical fiber transmission and the PMD adaptive compensation is required urgently. An experiment of two-stage adaptive compensation for polarization mode dispersion in a 40 Gb/s RZ optical time-division multiplexed (OTDM) communication system is reported. The particle swarm optimization (PSO) algorithm with the six degrees of freedom (DOF) is adopted to maximize the degree of polarization (DOP) and realizes the adaptive PMD compensation. The compensation process is completed within several hundred milliseconds. The method of Poincaré sphere (PS) is applied to measure the PMD values in the experimental fiber link. The results show that the DGD decreases from 21 ps to 1.3 ps and the second PMD descends from 266 ps2 to 43.5 ps2 in central wavelength of 1560.5 nm. The first and second order PMD are compensated together in different degree and the whole system power penalty is less than 1 dB (@BER 10-9) after PMD adaptive compensation.