Central Asian Orogenic Belt (CAOB) is one of the largest accretionary orogenic belts in the world. The eastern segment of CAOB is dominated by Paleozoic Paleo Asian Ocean tectonic regime, Mesozoic Paleo-Pacific tectonic regime and Mongolian-Okhotsk tectonic regime. The Songliao and Jiamusi blocks are located in the easternmost part of the CAOB and are the key region to solve the problem about overprinting processes of multiple tectonic regimes. It is generally believed that the Mudanjiang Ocean between the two blocks was finally closed in the Mesozoic, but the Paleozoic magmatism also developed along the Mudanjiang suture zone, while on both sides of the suture zone, there were comparable Paleozoic strata, indicating that the two blocks had converged during the Paleozoic, and the evolution history of the two blocks in the Late Paleozoic remains controversial. The Carboniferous-Permian terrestrial strata mainly developed in Binxian, Wuchang and Tieli on Songliao Block, Baoqing and Mishan on Jiamusi Block. Samples from the Songliao and Jiamusi blocks in the Late Carboniferous-Early Permian and Late Permian are collected for comparative analysis. The LA-ICP-MS zircon U-Pb dating results show that the maximum depositional age of Middle Permian Tumenling Formation and Late Permian Hongshan Formation in Songliao Block is ~260 Ma, while that of Tatouhe Formation and Carboniferous strata in Jiamusi Block are ~290 Ma and ~300 Ma, respectively, which supports the previous stratigraphic division scheme. The age peaks of ~290–300 Ma, ~400 Ma, ~500 Ma appeared in the Late Carboniferous to Early Permian strata of Jiamusi Block and the Middle Permian strata of Songliao Block. The age peak of ~500 Ma in the Middle Permian strata of Songliao Block may come from the Cambrian basement, Mashan Complex, of Jiamusi Block, while the age peaks of ~420–440 Ma in the Carboniferous strata of Jiamusi Block may come from the Silurian magmatic arc in Zhangguangcai Range in the eastern margin of Songliao Block, reflects the history that they had been potential sources of each other, indicating that they may have combined in the Paleozoic. The Hongshan Formation of Songliao Block in the Late Permian lacks the age peak of ~500 Ma, which indicate that Jiamusi Block was not the provenance of Songliao Block in the Late Permian, that is, there was a palaeogeographic isolation between the two blocks. Combined with the ~210 Ma bimodal volcanic rocks developed along the Mudanjiang suture zone reported previously, we believe that the oceanic basin between the Songliao and Jiamusi blocks should have been connected in Late Permian and reopened during Late Permian to Late Triassic.