The invention relates to the technical field of image mosaicing, in particular to a method for mosaicing heterogeneous images and a system thereof. The method for mosaicing the heterogeneous images comprises the steps of mosaicing more than one pixel input stream, firstly saving each pixel input stream into a frame cache module, mosaicing each frame of data in a cache sub-module through a mosaicing device and sending to a user port, and the method further comprises the following steps: (1) detecting more than one pixel input stream of images generated by a display card, and determining the pixel input stream with slowest rate; (2) carrying out processing of reducing frame rate on the multiple pixel input streams according to information of the pixel input stream with the slowest rate, and getting multiple pixel input streams after frame-reducing processing; and (3) mosaicing the multiple pixel input streams after the frame-reducing processing, getting image data after mosaicing and frame-reducing processing and sending to the user port. By adopting the invention, the phenomena of screen flicker, instantaneous screen noise and the like during the mosaicing caused by inconsistent frame rates among the multiple pixel input streams can be effectively reduced.