This work tries to improve the effective throughput as well as to achieve better fairness of the transport protocol with efficient selective retransmission scheme. The commonly used transport layer protocol, transmission control protocol (TCP), has been developed for more than two decades, but its retransmission scheme is hard to be satisfactory. However, service specific connection oriented protocol (SSCOP) provides an excellent retransmission mechanism with poor flow control function. When the lower layer protocol is Asynchronous Transfer Mode, using SSCOP instead of TCP/IP over AA5 to provide transport layer service can specifically reduce the protocol overhead. We propose a scheme for SSCOP to enhance its flow control performance. This scheme combines the rate-based flow control with the queuing delay control. The simulation result shows that our enhanced SSCOP achieves both higher throughput and better fairness. It demonstrates that a proper flow control scheme with efficient selective retransmission is crucial for optimizing the performance of a transport protocol.