Aiming at the problem of huge computation in pulsar period estimation methods, a direct pulsar period estimation algorithm was proposed. Based on the discussion of the influence of period errors on pulse time of arrival estimation methods, the mathematical model of the said period estimation method using TOA information is derived. In this method, a set of photon time of arrivals(TOAs) is divided into several segments in an equal time interval, and TOA information corresponding to each segment is calculated using time domain methods. According to the formula of the TOA information and period error, the Least Square method is adopted to estimate the period. A new intuitionistic criterion for the precision of pulsar period is developed by the value of the slope of the φ－t graph, which is different from the scheme that searches the perfect period based on maximum peak principle. Theoretical analysis and the results of experiments utilizing physical and numerical data are demonstrated that the presented pulsar period estimation method can achieve a precise and high-resolution period from a short observation of photon time of arrivals, which can help to realize the engineering application of X-ray pulsar navigation.