The invention discloses a phase noise compensation method, module and system of a CO-FBMC system, and belongs to the field of optical communication. The compensation method comprises the following steps: performing first unscented transformation on posterior estimation of phase noise at a previous moment to obtain an initial Sigma point set, approximating a priori estimation value of the phase noise at the current moment according to the initial Sigma point set, performing second unscented transformation on the priori estimation value to obtain a multiplied Sigma point set, substituting the multiplied Sigma point set into a nonlinear equation for iteration, and obtaining a multiplied Sigma point set; and solving to obtain an estimated mean value and a covariance of the FBMC symbol at the current moment, calculating a Kalman gain matrix according to the estimated mean value and the covariance, and obtaining a posteriori estimated value of the phase noise at the current moment according to the Kalman gain matrix. The invention also provides an unscented Kalman filter compensation module and a CO-FBMC system. According to the method, a nonlinear equation does not need to be approximated to a linear equation, and the method has higher phase noise tolerance under the same precision. Meanwhile, a Jacobian matrix does not need to be solved, and the calculation amount is greatly reduced.