Abstract Zircon fission-track (ZFT) analysis was performed on 12 samples, which were collected at the depths between 300 m and 1133 m in different structural units of the Huaibei coalfield in eastern China. The ZFT dating and decomposition results indicate the age populations can be divided into three periods, which are 213 ± 21 Ma–230 ± 21 Ma, 252 ± 32 Ma–304 ± 21 Ma and 378 ± 39 Ma–933 ± 16 Ma. These periods are less than, close to and greater than the depositional age, respectively. The continental collision between the north and south China plates impacted on its thermal and structural evolution strongly, but it is possible the burial and magmatism merely resulted in partial annealing on ZFT. Obvious differences of structural and thermal evolution exist in both the EW and NS directions. And the differences in the EW direction were mainly resulted from the tectonic movements in late Indosinian and Yanshanian, but the NS direction differences were on account of the magmatic activity in Yanshanian.