A method of filtering overlay data by field is provided in the present invention. The method includes the following steps. A minimum number of measure points per field on a semiconductor substrate is decided. Field data filtering rules are set. Overlay raw data is inputted. A raw data filtration is performed to the overlay raw data by field according to the field data filtering rules. Modified exposure parameters are generated for each field according to overlay data of remaining measure points per field after the raw data filtration when the number of the remaining measure points per field is larger than or equal to the minimum number of the measure points per field. Accordingly, the modified exposure parameters will be more effective in reducing the overlay error because more outliers may be filtered out before generating the modified exposure parameters.