The invention relates to a controlling method of waypoint flow. The controlling method of the waypoint flow comprises establishing a time slice containing a plurality of time ranges according to a time sequence, initializing the time ranges, enabling each time range to be in an open and free state, setting the pass frequency of a waypoint in different time ranges according to the flow control information of the waypoint, adjusting width of different time ranges according to the passing frequency, and marking the opening-closing state of the time range corresponding to the pass frequency to be a closed state when the passing frequency is zero. The controlling method of the waypoint flow describes and controls the trafficability characteristic of an aircraft of the waypoint at a specific time through the width change, the opening-closing change, and the free-non-free change of the time slice, is suitable for different flight sort algorithms, namely, can carrying out flexible sorting according to the properties of different aircrafts, and is easy to control and high in precision, and therefore the flow control of the waypoint can be effectively achieved, and conflicts are prevented from occurring.