According to the comprehensive research achievements of stratigraphy such as biostratigraphy, magnetostratigraphy (ESR dating method), seismic stratigraphy and sequence stratigraphy and by means of the recognition of regional isochronous sequence boundaries, the analysis on boundary orders and the correlation of boundary properties in the faulted basin, a regional isochronous sequence framework of the Paleogene in Jiyang Depression is established on the basic unit of third-order sequences. Then the analysis on the comparison of  all second-order sequences and major subtle reservoirs which were developed in the third-order sequences in the four sub-depressions of the Jiyang Depression shows that the second-order sequences are directly controlled by tectonic episodes, therefore, they are similar in characteristics. The cyclicity of major third-order sequence stratigraphic framework coincides to each other among the four sub-depressions, with the marker sediments developed in the same or similar cycle positions. However, the third-order sequence boundary properties of T2, T4, and T6 are apparently different among different sub-depressions. According to the sequence genesis dynamics, the consistency of cycle properties and the difference of boundary properties indicate respectively that the sedimentary environments control the sediment types in the same sequence stratigraphic framework and the migration of tectonic depocenters and sedimentary centers in the Bohai Bay Basin controls the sequence boundary properties.