The measurement data from Time-Keeping system can not totally show the performances of an atomic clock for the various factors. So, it is necessary to make a research on the error checking and correction algorithm. In this paper, the commonly used method is analyzed firstly, and then a new error checking and correction algorithm is put forward with the statistical method. At last, the new algorithm and the commonly used method on the measurement data process is compared by using the data from the National Time Service Centre's time-keep system, and the result show t the new algorithm is efficient.