The invention discloses a moving point target detection method and system based on high-time-phase detection, and the method comprises the steps: obtaining an image sequence shot by a high-frame-frequency camera, and dividing the image sequence into a plurality of basic processing units; in each basic processing unit, detecting a pixel with a target by using time domain transient fluctuation information caused when the target passes through the pixel to obtain a track of the target; and associating the target tracks of all the basic processing units through a track association method to obtaina target overall track. According to the method provided by the invention, a high-frame-frequency detection data and time sequence processing method is utilized, so that the detection accuracy of thelow-signal-to-noise-ratio moving point target can be improved, and the false alarm rate is reduced.