Policies on aging have been insufficient in terms of gender and life cycle. In particular, no research has been conducted that attempts to understand the trajectories of different biological aging processes between men and women according to age at the population level. Therefore, using nationally representative data accumulated over a long period and the allostatic load, an objective biological aging indicator, this study aims to (1) present the trend of the health gap between men and women over the past 20 years, (2) assess the gap between men’s and women’s health according to age, period, and birth cohort through the latest hierarchical age-period-cohort (HAPC) modeling to solve the identification problem, and (3) investigate the cause of the gap using Oaxaca-Blinder decomposition. Our results found that biologically, men had worse average health over the life cycle than women. Second, through the HAPC analysis, it was confirmed that the health trends and trajectories of men and women differed according to age, period, and birth cohort. Decomposition analysis confirmed that socioeconomic characteristics and health behavior factors were the main factors contributing to the gap. A birth cohort-based policy was proposed based on APC studies in health and aging, as well as timely prevention and intervention of aging-related chronic diseases.