A method and an apparatus for generating an image with shallow depth of field, suitable for a three-dimensional imaging system having a left lens and a right lens, are provided. First, the left lens and the right lens are used to capture a left-eye image and a right-eye image. Next, a disparity between each of a plurality of corresponding pixels in the left and right-eye images is calculated. Then, the depth information of each pixel is estimated according to a focus of the left and right lens, a lens pitch between the left lens and the right lens, and the calculated disparity of each pixel. Finally, the pixels in the left-eye image and the right-eye image are blurred according to the focus of the left lens and the right lens and the estimated depth information of each pixel, so as to obtain the image with shallow depth of field.