This paper presents an analytical model of a cross-layer communication system to enable improvement in the Transmission Control Protocol (TCP) over mixed wired and wireless Internet. The focus is on the quantitative performance evaluation of the interactions between TCP NewReno and a hybrid Automatic Repeat reQuest protocol (HARQ) in the link layer (LL) with a finite buffer size. The significant improvement in TCP NewReno throughput when HARQ adaptively selects its optimal settings according to explicit cross-layer information is shown. Through ns-2 simulations, it is demonstrated that this proposed analytical model accurately predicts the TCP-HARQ system performance.