Ontake Volcano in central Japan was last active from ~ 100–35 Ka. The eruptions contained rhyodacite pumice and lavas in the first stage (stage O1, > 33 km3), followed by eruptions of andesite lavas and pyroclastics (stages O2 and O3, > 16 km3). Modeling of major and incompatible elements with Sr isotope ratios suggests that the primary magma was a high‐alumina basalt. One andesite magma type appears to have evolved from the basalt in a closed system magma chamber, in part by fractional crystallization, and its generation included crustal assimilation. The other andesite magma type is considered to have evolved in an open system magma chamber in which repeated input of primary magma occurred together with wall‐rock assimilation and fractional crystallization. The rhyodacite is inferred to have evolved in a closed system magma chamber by fractional crystallization of the second type of andesite. These genetic relationships require that the magma chamber functioned alternately as an open and a closed system. Geobarometry indicates that there may have been multiple magma chambers, located in the upper crust for the rhyodacite, near the upper–lower crust interface for the andesite and in the mid‐lower crust for the basalt. These chambers were stacked to form the magma plumbing system of Ontake. Incompatible element compositions of the basalt are considered to have changed during the eruptions, suggesting that two different plumbing systems for stage O1 magma and for stages O2, O3 magmas existed during the 65 Ka of activity. Evolutionary history of the systems implies that the primary magma was introduced into the magma plumbing system each for ~ 17 500 years and that the life span of a magma plumbing system was shorter than 40 Ka.