The invention discloses an effective heart rate measuring system capable of resisting natural motion of the head. The effective heart rate measuring system comprises two processing units, wherein a first unit is used for obtaining stable ROIs, a photographic lens is opened, real-time images are converged, the system can automatically detect and trace human faces and face feature points, and afterthe human faces are detected, a search frame is narrowed according to a human face golden ratio so as to increase the tracing speed; and the positions of regions of interest ROIs are respectively designed on foreheads, right cheeks and left cheeks, the pose (pose) of head motion is judged through the face feature points, accordingly the appropriate ROI is automatically selected, and through motionwave filtering, stable ROI signals are obtained. The second unit is used for processing heart rate signals, the ROI signals are firstly preprocessed, green channels are taken out from the ROIs to besubjected to pixel averaging, the average value of each time point is in series connection to form a time sequence signal, then through standardization processing, the influence of ray changes on thequality of the signals is eliminated, main signals are highlighted, and through quick Fourier transformation and bandpass filtering processing, heartbeat data can be calculated.