Zircon fission-track length is an essential parameter for studying annealing behavior. Based on measured data from sedimentary basin samples with different thermal backgrounds, this study investigated the annealing behavior of zircon fission tracks and discussed the factors influencing the fission-track length. The results show that the fission track of the Sk1 sample has a negative correlation with the angle to the C-axis on the fission track; specifically, a smaller angle corresponds to a longer track length, while a larger angle results in a shorter track length. The angle to the C-axis on the fission-track of the Sk1 sample was mainly distributed at 10°~70°, and the overall distribution was relatively random. The Ku1 samples were primarily distributed at high angles (60°~90°), and the overall distribution was not random. The initial annealing temperature of zircon fissions track in the sedimentary basin of Sk1 is 220 °C, and the average track length of deep samples is 5.02~5.55 μm. The initial annealing temperature of the zircon fission track in the sedimentary basin of Ku1 is 170 °C, and the average track length of deep samples is 8.06~8.31 μm. Under a high temperature and thermal background, the temperature at which the zircon fission track of Well Sk1 was affected by the sedimentary basin was higher than that of Well Ku1. The difference in initial annealing temperature and annealing behavior of zircon fission tracks with different thermal backgrounds is attributed to variations in the heating rate. The average track length of the middle and shallow samples in well Sk1 is 5.85~8.36μm; the average track length in the Ku1 well is 9.21~10.05 μm. The minimum age of shallow samples in both wells exceeded the formation age, indicating that they were not affected by the sedimentary basin. Instead, the shortened track length was affected by thermal events in the source.