Following the TCP and UDP, stream control transmission protocol (SCTP) has become a new transmission layer protocol. This protocol is a connection-oriented reliable transmission protocol, with the features of multiple hosts, multiple streams, and so on. Because of its excellent properties, SCTP is also widely used in IP network to transmit signal. Based on the SCTP protocol, this paper proposes a new calculation model for throughput, and then uses network Simulation tool NS2 to improve the calculation model, confirming that this model can effectively calculate the throughput of the SCTP protocol.