Abstract: A system and a method for imputing missing values and a computer program product thereof are applicable to a data matrix. The system includes a storage unit having the data matrix and a computing device. The computing device finds complete and incomplete data transactions from the data matrix, finds at least one target data transaction approximate to each incomplete data transaction from the complete data transactions, and obtains known data at corresponding positions to compute an initial estimated data to replace unknown data. Then, a correction data transaction containing the initial estimated data is selected from the incomplete data transactions, a rough set of the selected initial estimated data is found in a manner of grouping same data into one group, and a numerical value correlated to the initial estimated data is found and used to compute an imputed data, so as to impute the imputed data into the original estimated data.