high power diode laser arrays have found increasing applications in the field of pumping solid-state lasers and fiber lasers. due to the thermal crosstalk across diode laser arrays and non-uniformity of local flow rate within microchannel cooler, junction temperature distribution becomes inhomogeneous, consequently leading to spectrum broadening and large beam divergence of diode laser pumping sources. in this work, an analytical method and numerical heat transfer based on finite volume method were employed to optimize the inner structure of microchannel cooler so as to obtain low thermal resistance and uniform junction temperature distribution for the diode laser arrays. three-dimensional numerical models were developed to study the fluid flow and heat transfer of copper stacked microchannel coolers with different dimensions and arrangements of inner channels and fins. more uniform junction temperature distribution of diode laser array package could be achieved by self-heating compensation with specific coolant covering width. these results could provide significant guidance for the design of microchannel coolers of high power diode laser arrays for better performance. © 2017 spie.