Based on the theory of sequence stratigraphy and sedimentology, the characteristics of sequence stratigraphy and sedimentary facies of Mesozoic in northern Bonaparte Basin are studied. The Mesozoic formation can be divided into four second-order sequences and nine third-order sequences, which is classified into two kinds of sequence combination. The lower and middle sequences are dominated by descending cycle, which belongs to typical regression series, while the upper sequence is dominated by rising cycle, which belongs to transgression series. The sedimentary environment changed frommarine facies to fluvial facies then transitional delta facies, eventually neritic facies, forming a whole set of regression and transgression cycle. Finally, it is pointed out that the shore in the eastern slope and the delta and the shore in the Sahul platform are the favorable exploration belts.