Micropores of nickel-based superalloys are inevitably formed during solidification and heat treatment, decreasing the high-temperature mechanical properties. Therefore, controlling the contents of micropores by hot isostatic pressure (HIP) and revealing the corresponding effect on mechanical properties have been the research focus of few papers previously. In order to investigate the effect of HIP on micropores and low-cycle fatigue (LCF) of a second-generation nickel-based SX superalloy, two heat treatment routes were carried out for as-solid-solution (AS) states in this study. The effect of HIP on micropores and 760 °C fatigue properties of the experimental alloy was analyzed, and the crack initiation and propagation mechanism were also discussed. HIP can significantly increase the LCF life by changing the crack initiation and propagation. The fatigue mechanism associated with the relationship between microstructure and mechanical property will be discussed. This study will be helpful to optimize the heat treatment regime with HIP and improve high-temperature mechanical properties of nickel-based SX superalloy.