A correlation processing method based on observation data from the Deidou satellite includes steps of: a) collecting observation data from the BeiDou Navigation Satellite System; b) capturing data samples according to the observation data, and determining a membership degree of each data sample, and the data samples are classified; c) constructing a target classification function, and selecting the data samples to remove the unavailable data samples; and testing stationarity of each time series; d) building an observation model by using data samples having stationarity in step c), and determining correctness of the observation model and optimizing the observation model if the observation model is not correct; and e) searching a correct observation model obtained in step d) for correlation data, and performing correlation analysis of the observation data. The method of the present invention improved the quality of observation data can be effectively improved.