The disclosure provides a method and system for correcting density data at end of a pop-up filter rod, and the method comprises the following steps of acquiring a microwave method measurement value ofthe filter rod; selecting standby data; calculating an average value of the density values of each measurement unit, calculating an average value of each average value, the standard deviation and theminimum value that may occur, determining the distortion and the measurement unit to be modified according to the calculated value; performing a regression analysis by using the array consisting of the detection values of a first undistortion measurement unit at the beginning or/and the end of the filter rod as the dependent variable, and using the array consisting of the detection values of thefirst distortion measurement unit at the beginning or/and the end of the filter rod as the independent variable, using the obtained regression function as a preliminary correction mathematical model of the distortion unit for correction; recording the corrected detection values, reconstructing the independent and dependent variables, performing regression analysis to obtain a regression function and a determination coefficient, determining the regression function with the largest determination coefficient as the modified mathematical model of the distortion unit, and modifying the data according to the modified mathematical model.