Providing Internet services is very important in 3G networks. TCP is the transport layer protocol used by the majority of the applications on the Internet. We studied the performance of TCP when utilizing link layer retransmission (e.g. RLP in IS95 and IS2000) and MAC layer retransmission in CDMA system. There is not much work on how retransmissions in these layers can work together and how the performance of TCP with RLP and MAC retransmissions would be. In this paper we propose an analytical model for RLP performance when MAC retransmission is presented in this architecture. We also studied the performance of TCP based on RLP and MAC with extensive simulation experiments. We study in detail the interactions between different layers and characterize the performance using delay distributions and throughput. Our results show significant improvement in TCP performance with MAC layer retransmission. For example, for packet loss rate of 0.1, the TCP packet delay is reduced by 20.94%, and throughput is increased by 39.57%.