Seismic data analysis is mainly dealt with by difference mathematic method. Based on the water level data of Tengchong well and Chuan No.05 well in 2011 and 2015, five kinds of difference methods of MapSIS software are applied to extract, analyse the abnormal data, transform and map the data. They are arithmetic difference, value absolute difference, absolute sum sequence, cumulative sequence of difference anomaly energy and difference anomaly frequency. Further, the water level anomaly characteristics which are caused by the M W 9.0 earthquake in Japan and the M S 8.1 earthquake in Nepal are analysed, and the causes of the abnormal water level characteristics are discussed.