A method of correcting distortion caused by fingerprint input sensors of heterogeneous fingerprint recognition systems. The method includes a first step of fabricating a measurement pattern for measuring resolutions of a fingerprint input sensor, a second step of measuring image resolutions of an image, acquired by the fingerprint input sensor, using the fabricated measurement pattern for predetermined locations and directions, a third step of designing control lines for compensating for the distortion caused by the fingerprint input sensor, based on the measured resolutions, a fourth step of obtaining average horizontal and vertical resolutions of the acquired image, a fifth step of modeling the control lines based on a ratio of the average horizontal resolution to the vertical average resolution, and a sixth step of compensating for the distortion of the acquired image based on results of the modeling.