The most common age constraint for the diatomaceous sediments is biostratigraphy of siliceous microfossils. Although biostratigraphy is a powerful tool to establish stratigraphy and correlate with sedimentary sequences in other sites, biostratigraphy generally includes uncertainties difficult to evaluate. In this study, we measured zircon U–Pb ages of eight tuff beds intercalated with diatomaceous mudstone of the Nakayama Formation on Sado Island in Central Japan and integrated the U–Pb ages with diatom and radiolarian biostratigraphy, whose ages and errors were re-evaluated by this study, to establish an age model precisely representing the sedimentary age. Two tuff beds in the upper and middle part of the formation offered zircon U–Pb ages of 6.7 ± 0.2 Ma and 10.87 ± 0.07 Ma, which are consistent with biostratigraphy, and provided a good example of effective integration of zircon U–Pb ages with the biostratigraphy. On the other hand, zircon U–Pb ages of the other six tuff beds in the lower part are around 12 Ma and not distinguishable from each other. In addition, older zircon grains in the 6 tuff beds are assembled in the interval from 30 to 20 Ma, which is consistent with the age of the volcanic basement rocks forming most part of Sado Island. Similarities in chemical compositions of glass shards and age distributions of zircon grains indicate that the volcaniclastic components in the tuff beds should originate from single or associated magmatic activities.