The invention discloses a marking method based on explicit congestion notification (ECN) in a multi-queue data center environment, and mainly solves the problem that a traditional ECN cannot sense micro burst flow and cannot adapt to a dynamic network. The method mainly comprises three parts, namely ECN threshold lower bound calculation, threshold base value setting and threshold dynamic adjustment. According to the method, firstly, steady-state analysis is carried out on the generation and transmission process of the micro burst flow in a multi-queue data center environment, the lower bound of an ECN threshold value is solved for each switching queue, and it is guaranteed that a switch queue buffer area can effectively absorb the micro burst flow. Then, based on an ideal Generic Packet Schedule (GPS) model, an ECN threshold lower bound is adjusted, a threshold base value is set for each queue, it is guaranteed that the enqueue rate and the dequeue rate of exchange queues are balanced,finally, an optimization model for queue buffer maximum utilization is established for switch memory resources on the basis of the target of improving the network throughput, and an ECN threshold dynamic adjustment algorithm is provided.