This paper analyzes the physical layer security performance of hybrid automatic repeat request (HARQ) systems with the assistance of an intelligent reflecting surface (IRS) and aims to reveal the primary factors that enhance PLS. First, closed-form expressions for the connection outage probability (COP) and secrecy outage probability (SOP) in HARQ with chase combining (HARQ-CC) are acquired using the generalized-K (KG) distribution. Then, these two critical metrics are derived while adopting HARQ with incremental redundancy (HARQ-IR), resorting to the mixture gamma (MG) distribution and the Mellin transform. Diversity and coding gain are also addressed through an asymptotic analysis of the COP and SOP. Finally, an evaluation of the numerical results demonstrates that a greater gain in the main channel and the wiretap channel can be produced by increasing the number of meta-surfaces rather than increasing the maximum transmission number, except for the higher signal-to-noise (SNR) region of HARQ-IR where the latter is preferred. This finding provides a significant guidance for the joint configuration of IRS and HARQ to achieve secure communication.