In this paper, several kinds of numerical simulations of three-dimensional stacked package with different microchannel coolers have been carried out to compare the heat dispersion performance. By setting different parameters of inlet flow and the power of two chips, it shows that: The overall temperature of 3-D stacked package with prism array microchannel is lowest of all at the same rate of flow and power. The 3-D stacked package with prism array CNT's microchannel cooler has been found to have the best heat dispersion performance.