The invention discloses a network traffic application identification method, system and equipment, and a computer readable storage medium. The method comprises the following steps: obtaining encryptednetwork traffic data; extracting flow characteristics of the encrypted network flow data; and obtaining an application identification result of the encrypted network traffic data according to the traffic characteristics. According to the method, decryption operation is not carried out on the encrypted network flow data, the flow characteristics of the encrypted network flow data are directly extracted after the encrypted network flow data are obtained, and application identification is carried out according to the flow characteristics. The extraction of the flow characteristics is directly based on the encrypted network flow data instead of the plaintext content of the encrypted network flow data, so that the equipment only acquires the encrypted network flow data and the flow characteristics without knowing the plaintext content of the network flow data even if the equipment generates a security problem. Therefore, according to the network traffic application identification method provided by the invention, the security of encrypted network traffic data application identification is improved.