The invention discloses a flow compensation method for a nuclear magnetic resonance imaging system. The flow compensation method is characterized by comprising the following steps that: (1) gradient combined pulses which satisfy flow compensation are applied in a frequency encoding direction between a 90-degree radio frequency pulse time series and a 180-degree radio frequency pulse time series of a fast spin echo (FSE) sequence; (2) a scattering gradient is applied before a signal acquisition gradient and before 180-degree radio frequency pulses, and a compensation gradient is applied after the acquisition gradient, and the signal acquisition gradient, the scattering gradient and the compensation gradient jointly form a first-order gradient velocity compensation gradient; (3) phase encoding gradient amplitude is set to be zero, and the time series of the sequence is set, and the amplitudes of the gradients are adjusted, and the amplitude of echo signal peaks of an echo chain is made to reach a maximum value, and the debugging of the sequence is completed; and (4) the sequence is outputted to a spectrometer, so that flow compensation can be realized. With the flow compensation method for the nuclear magnetic resonance imaging system of the invention adopted, situations such as cerebrospinal fluid flow and spinal fluid flow artifacts and image blurring can be significantly inhibited, and therefore, the problem of image artifact generation which is caused by physiological movement such as blood flow or periodic movement can be alleviated.