The Zhalantun terrane from the Xing’an massif, northeast China, was used to be considered as Proterozoic basements. However, amounts of detrital zircon ages from the meta-sedimentary rocks deny the existence of Precambrian basements recently. Notably, magmatic rocks were barely reported to limit the exact ages of the Zhalantun basements. In this study, we collected rhyolite, gabbro and quartz diorite for zircon in-situ U-Pb isotopic dating, which yield crystallization ages of ~505 Ma, ~447 Ma and ~125 Ma, respectively. Muscovite schist and siltstone define maximum depositional ages of ~499 Ma and ~489 Ma, respectively. Additionally, these dated supracrustal rocks and plutons also yield ancient detrital/xenocryst zircon ages of ~600–1000 Ma, ~1600–2220 Ma, ~2400 Ma, ~2600–2860 Ma. Based on the whole-rock major and trace element compositions, the ~505 Ma rhyolites display high SiO2 and alkaline contents, low Fe2O3T, TiO2 and Al2O3, and relatively high MgO and Mg#, which exhibit calc-alkaline characteristics. These rhyolites yield fractionated REE patterns and negative Nb, Ta, Ti, Sr, P and Eu anomalies and positive Zr anomalies. The geochemistry, petrology and Lu-Hf isotopes imply that rhyolites were derived from the partial melting of continental basalt induced by upwelling of sub-arc mantle magmas, and then experienced fractional crystallization of plagioclase, which points to a continental arc regime. The ~447 Ma gabbros exhibit low SiO2 and alkaline contents, high Fe2O3T, TiO2, MgO and Mg#. They show minor depletions of La and Ce, flat MREE and HREE patterns, and negative Nb, Ta, Zr and Hf anomalies. Both sub-arc mantle and N-MORB-like mantle were involved in the formation of the gabbros, indicative of a probable back-arc basin tectonic setting. Given that, the previously believed Proterozoic supracrustal rocks and several plutons from the Zhalantun Precambrian basements were proved to be Paleozoic to Mesozoic rocks, among which these Paleozoic magmatic rocks were generally related to subduction regime. So far, none Proterozoic rocks have been identified from the Zhalantun Precambrian basement, though some ~600–3210 Ma ancient detrital/xenocryst zircons were reported. Combined with ancient zircon ages and newly reported ~2.5 Ga and ~1.8 Ga granites from the south of the Zhalantun, therefore, the Precambrian rocks probably once exposed in the Zhalantun while they were re-worked and consumed during later long tectonic evolutionary history, resulting in absence of Precambrian rocks in the Zhalantun.