Based on the integrated research of outcrops, wells and seismic data, one magasequence and four third-order sequnces and nine system tracts have been identified in the Middle-Lower Jurassic of the Northeast Junggar Basin, Xinjiang, China. Different from the marine sequence, there are four types of system tracts recognized which are lacustrine transgressive system tracts (TST),lacustrine regressive system tracts (RST), highstand system tracts(HST) and alluvial system tracts(AST). The main factors controlling sequence development are tectonics and lacustrine regression or transgression, which controlled the sequence stratigraphic features. Sequence boundaries SB1, SB3 and SB5 were formed under the faster lacustrine regression and active tectonic setting, SB2,SB4 and system tracts RST2 and RST4 under the gently lake regression and weak tectonic setting, TST1 and TST3 under the faster lacustrine transgression and active tectonic setting, HST under the stable both lake water and tectonic and AST during alluvial deposit after extinct lake. There are good reservoirs in the retrograding braided delta depositional system among the TST, in which porosity is about 20% and permeability about 200 mD. Under the lake transgression and provenance uplift, the braided delta depositional system was developed in the transformed zone between the alluvial depositional system and the lacustrine depositional systems, because of the strong water energy, most of the matrix can be sorted off. The lacustrine mudstones among the HST is good source rocks, especially the mudstone of HST3 is typical condensed section, which is pure and its thickness is about one hundred meters. The multi-superimposed HST and TST created good source-reservoir-cap assemblages.