The invention discloses a long sequence automatic interferometry system and method, including a storage, an instruction acquisition module, a data preparation module and an automatic processing module. The data preparation module includes a raw data acquisition module, a crawler module, a data format conversion module and a target area digital elevation model generation module. The automatic processing module includes a main image selection module, a registration resampling module, a permanent scatterer point extraction module, an optimal interference network generation module, an interferencefringe pattern generation module, a target interference fringes generation module and an analysis module. The long sequence automatic interferometry system and method can integrate differential interferometry and permanent scatterer processing, achieve the automatic processing of SAR data through standardized customization for a processing procedure, do not require manual intervention, do not require a complicated learning process when users use, are simple and convenient to operate and reduce threshold of the users. Meanwhile, the long sequence automatic interferometry system and method canachieve parallel computing of various phase analysis and achieve high efficiency in data processing.