The invention discloses an integer pixel precision motion estimation method and a system for the same. The method comprises the following steps of: dividing the search window data into 16 types of pixels and respectively storing the data into 32 RAMs (Random Access Memories) according to the parity of macro blocks, using 16 dual 4*4 pixel motion cost arithmetic units to respectively calculate the motion estimation cost of each type of pixels, and then, when performing layered searching, distributing and combining the arithmetic units, scanning macro block columns one by one according to a dual 'arch'-shaped mode, and realizing layer-by-layer incremental search of which step sizes are respectively 4, 2 and 1. According to the method, by means of referring to a data window storage and management mechanism, pre-storing a score precision search window and the like, the access bandwidth of an external memory is reduced, the bandwidth utilization rate of an internal memory is improved, the degree of parallelism of motion search is improved greatly, and the execution efficiency of large-scale search motion estimation is improved. Simultaneously, the complexity in implementation of layered search hardware is reduced, and the chip area is saved.