Process noises and measure noises exist in flight test data, which lead to incompatibility of flight data. To solve the problem that output error method the popular method used in flight test data compatibility checking is not fit for helicopter model and fixed plane lateral model data compatibility checking with serious coupling. Firstly, extended Kalman filter is applied for states estimation. Next, compatibility analysis for results of extended Kalman filter is carried on by way of output error method. By this technology, problems of wave filtering errors which are caused by externed Kalman filter primary convergence are solved, and problems of time delay modification by hand in output error method is conquered and inconvergence of output error method when errors in measuring data are big are solved , respectively. Verification effect and computational efficiency are greatly improved.