In a hybrid automatic repeat request with chase combining (HARQ-CC) system, we analyze physical layer secure performance and determine the secrecy redundancy rate by proposed quasi-concave optimization methods with effective secrecy throughput (EST) criteria. First, key performance metrics, including connection outage probability (COP), secrecy outage probability (SOP), EST, and delay, are discussed. Then, under the constraint of COP, we optimize the secrecy redundancy rate to maximize the EST, which is a quasi-concave function, by both the bisection and fixed-point methods. Furthermore, under the simultaneous constraints of COP and SOP, the bisection and Lagrangian multiplier methods are applied to optimize the secrecy redundancy rate. From the comparison of the numerical and simulated results, it is concluded that EST demonstrates practical secure performance of HARQ-CC, and the proposed optimization methods adjust the secrecy redundancy rate for improved security.