Abstract To determine how local geological events contributed to the evolution of accretionary complexes and eventual exposure of rocks with different structural levels, geochronological mapping was carried out using fission track (FT) analysis at the Kii Peninsula, southwest Japan. At this site, the original zonal structure of Cretaceous accretionary complexes parallel to the subduction zone is disturbed by the northward projection of the Shimanto accretionary complex. Twenty‐six zircon FT ages were obtained from an area of ∼12 km in an east–west direction and ∼15 km in a north–south direction, and classified into three groups: (i) ages ∼15 Ma (range ∼10–20 Ma), which are distributed along the northwest–southeast valley; (ii) ages of ∼50 Ma in the northwest of the study area; and (iii) ages older than those in Groups 1 and 2. Based on results from eight zircon FT length distributions, the Miocene ages appear to be the result of spatial variations in heat influx and cooling after the regional exhumation of the area, as recorded by FT ages of ∼50 Ma.