The invention relates to a trajectory data-based signal intersection periodic flow estimation method. The method comprises the following steps that: 1) the trajectory point data of sampled vehicles are acquired, and the key point information of the vehicles entering and leaving a queue is obtained; 2) a fitting method is adopted to estimate the queuing waves and evanescent waves of vehicle queuing, and the intersection point of the queuing waves and the evanescent waves is taken as the flow estimated value of queuing vehicles; 3) the density distribution function of full-cycle flow is obtainedaccording to the flow estimated value, and the proportion of non-stop vehicles in the full-cycle flow; and 4) a full-cycle flow estimation problem is transformed into a parameter estimation problem based on the Poisson distribution and M3 distribution of the non-queuing vehicles according to the density distribution function of the full-cycle flow, and a maximum likelihood estimation method is used to perform estimation, and the maximum-likelihood expectation-maximization method is adopted to perform solving, and the estimated value of the arrival flow of each cycle can be obtained. Comparedwith the prior art, the method of the present invention has the advantages of the fusion of model analysis and statistical analysis, the full use of trajectory information, wide applicability and thelike.