The invention relates to a rotor flux on-line identification method and a system for a permanent magnet synchronous motor. The method includes: S1, respectively obtaining a previous rotor flux value and an intermediate variable value; and S2, putting the obtained previous rotor flux value and the intermediate variable value into a rotor flux calculating formula, and calculating the current rotor flux value. According to the method and the system, a classic dq-axis mathematical model is employed, a recurrence least square method is employed, the state of the rotor permanent magnet can be effectively obtained via the estimation of the rotor flux, the phenomenon of demagnetization due to over-high current is effectively prevented, the problem of frequency shutdown is prevented, and the related complaint problem of consumers is solved; the realization is simple, the calculation amount is small, any hardware cost is not needed, large-area engineering practice and promotion can be realized, and the method and the system are applicable to the permanent magnet synchronous motors of different kinds.