Taking Beijing-Shanghai High-speed Rail as an example, this paper makes an analysis about the impact of city scale, distance, departure frequency upon the intensity of passager flow between cities, and decomposes the Time Saving effect of high-speed rail and departure frequency effect. A multiple liner regression model is constructed to analyze whether both effects are significant, under the control of the scale variable. The results show that Beijing-Shanghai High-speed Rail makes a readjustment of the passager flow between cities, leading to an decreasing impact of the scale variable upon the urban spatial interaction; the influence of the distance variable is significant in 2014, of which the absolute coefficient decrease, and which means passager flow is less sensitive to the spatial distance, leading to the increase of passager flow of the long-distance city-pairs. Therefore, the time saving effect of high-speed rail makes the distance less important for urban spatial interaction. The coefficient of the departure frequency variable is also significant in 2014, resulting from high-speed rail increasing the total departure frequency, and exalting the intensity of medium, medium-high departure frequency city-pairs, which means that the effect of departure frequency makes the departure frequency more important for urban spatial interaction.