A method for compensating time difference between images and electronic apparatus using the same method are provided. Input images are received by a plurality of image capturing units respectively. Each input image is checked to see whether a reference area and a reference area background are the same. When the reference area of the input image received from one of the image capturing units is not the same as the reference area background, a compensation image number is accumulated, and other input images are received continually until the reference area of each input image received from the image capturing unit is not the same as the reference area background. Afterwards, time difference between the input images received from a plurality of image capturing units is compensated according to the compensation image numbers.