The geometrical Modulation Transfer Function (MTF) of CMOS APS (active pixel sensor) is analyzed in this paper. Advanced APS have been designed and fabricated where different pixel shapes such as square, rectangle and L shape, were placed, because the amplifier circuit and other function circuits inter pixel of APS take up some pixel area. MTF is an important figure of merit in focal plane array imaging sensors. Research on analyzing the MTF for the proper pixel shape is currently in progress for a centroidal configuration of a target position. MTF will give us a more complete understanding of the tradeoffs opposed by the different pixel designs and by the signal processing conditions. Based on image sensor sampling and reconstructing model, the MTF expression of any active pixel shape has been deduced in this paper. According to actual pixel shape, three different active area pixels were analyzed, they were square, rectangle, and L shape, their Fill Factor (FF) is 30%, 44% and 55%, respectively. Results of simulation experiments indicate that different pixel geometrical characteristics contribute significantly to the figures of their MTF. Different geometrical shape of active sensitive area of pixel and different station in pixel would influence MTF figures. The analysis results are important in designing better APS pixel and more important in analyzing imaging system performance of APS subpixel precision system.