Five Paleogene volcanics sampled from the northern South China Sea were analyzed via LA-ICP-MS zircon U-Pb dating, including basalt and andesite from Borehole SCSV1 and volcanic agglomerate from Borehole SCSV2, respectively. A total of 162 zircon U-Pb dates for them cover an age range from Neoarchean to Eocene, in which the pre-Paleocene data dominate. The Paleogene dates of 62.5±2.2 Ma and 42.1±2.9 Ma are associated with two igneous episodes prior to opening of South China Sea basin. Those pre-Paleocene zircons are inherited zircons mostly with magmatogenic oscillatory zones, and have REE features of crustal zircon. Zircon U-Pb dates of 2518–2481 Ma, 1933–1724 Ma, and 1094–1040 Ma from the SCSV1 volcanics, and 2810–2718 Ma, 2458–2421 Ma, and 1850–993.4 Ma from the SCSV2 volcanics reveal part of Precambrian evolution of the northern South China Sea, well comparable with age records dated from the Cathaysia block. The data of 927.0±6.9 Ma and 781±38 Ma dated from the SCSV2 coincide with amalgamation between Yangtze and Cathaysia blocks and breakup of the Rodinia, respectively. The age records of Caledonian orogeny from the Cathaysia block are widely found from our volcanic samples with concordant mean ages of 432.0±5.8 Ma from the SCSV1 and of 437±15 Ma from the SCSV2. The part of the northern South China Sea resembling the Cathaysia underwent Indosinian and Yanshannian tectonothermal events. Their age signatures from the SCSV1 cover 266.5±3.5 Ma, 241.1±6.0 Ma, 184.0±4.2 Ma, 160.9±4.2 Ma and 102.8±2.6 Ma, and from the SCSV2 are 244±15 Ma, 158.1±3.5 Ma, 141±13 Ma and 96.3±2.1 Ma. Our pre-Paleogene U-Pb age spectra of zircons from the borehole volcanics indicate that the northern South China Sea underwent an evolution from formation of Precambrian basement, Caledonian orogeny, and Indosinian orogeny to Yanshannian magmatism. This process can be well comparable with the tectonic evolution of South China, largely supporting the areas of the northern South China Sea as part of southward extension of the Cathaysia.