In order to ascertain the secondary-order sequence boundary of Palaeogene in Jiyang depression, geophysical, geochemical and paleontological data were used to study and compare the feature of three boundaries of upper/lower Es4 (the fourth member of Shahejie formation), Es3(the third member of Shahejie formation)/ Es4 and Es4/Ek (Kongdian formation). Tectonic and paleo-environmental changes happened at the three boundaries have been investigated and the results can be concluded as follows: ①unconformity of upper/lower Es4 is more widespread and easier to identify compared with the unconformities of Es3/Es4 and Es4/Ek; ②tectonic stress characteristics indicated by fault activity modes and basin stretch directs were obviously different in the upper and lower Es4 but similar in the lower Es4 and Ek, the upper Es4 and Es3; ③climatic environment change happened at the upper/lower Es4 period was sharper than those happened at the Ek/lower Es4 and the upper Es4/Es3 period. It is ascertained that the order of upper/lower Es4 boundary is a secondary order, which is higher than those of Es4/Ek and Es3/Es4 boundary. Thus, there are three secondary-order sequences in Palaeogene which correspond to lithological stratum of Ek-lower Es4, upper Es4-lower Es2 (the second member of Shahejie formation) and upper Es2-Ed(Dongying formation) respectively. The new classification pattern of secondary-order sequence could not only give rational explanation to the lithological change in Es4 but also provide guidance to oil and gas exploration in Es4.