The invention provides a method and a system of flow control based on exchanger cache allocation. The method comprises the following steps: S1, initializing a domain of a congestion window in a packet before a sending terminal sends a data packet; S2, counting and maintaining total data flows N of a port with the exchanger; S3, when the exchanger receives the data packet, calculating the value of the congestion window of the data flow according to size of a caching pool at an outlet port; S4, comparing and determining the value of the congestion window; S5, sending the data packet to a receiving terminal with the exchanger, and sending a feedback packet to the sending terminal from the receiving terminal, wherein the feedback packet comprises the value of congestion window; and S6, when the sending terminal receives the feedback packet, giving the value of the congestion window in the feedback packet to the value of the congestion window of the sending terminal data packet. According to the invention, exchanger cache is allocated, and the bandwidth for each flow is distributed, which realizes the characteristics of quick convergence and less packet loss, and solves various problems due to great delay of short flow and packet loss.