Scientifically sound methods are essential to estimate the survival of trees, as they can substantially support sustainable management of natural forest resources. Tree mortality assessments have mainly been based on forest inventories and are mostly limited to planted forests; few studies have conducted age-based survival analyses in natural forests. We performed survival analyses of individual tree populations in natural forest stands to evaluate differences in the survival of two coniferous species (Abies sachalinensis (F. Schmidt) Mast. and Picea jezoensis var. microsperma) and all broad-leaved species. We used tree rings and census data from four preserved permanent plots in pan-mixed and sub-boreal natural forests obtained over 30 years (1989–2019). All living trees (diameter at breast height ≥ 5 cm in 1989) were targeted to identify tree ages using a Resistograph. Periodical tree age data, for a 10-year age class, were obtained during three consecutive observation periods. Mortality and recruitment changes were recorded to analyze multi-temporal age distributions and mean lifetimes. Non-parametric survival analyses revealed a multi-modal age distribution and exponential shapes. There were no significant differences among survival probabilities of species in different periods, except for broad-leaved species, which had longer mean lifetimes in each period than coniferous species. The estimated practical mean lifetime and diameter at breast height values of each coniferous and broad-leaved tree can be applied as an early identification system for trees likely to die to facilitate the Stand-based Silvicultural Management System of the University of Tokyo Hokkaido Forest. However, the survival probabilities estimated in this study should be used carefully in long-term forest dynamic predictions because the analysis did not include the effects of catastrophic disturbances, which might significantly influence forests. The mortality patterns and survival probabilities reported in this study are valuable for understanding the stand dynamics of natural forests associated with the mortality of individual tree populations.