Recently, the development trend of multi-module and multi-function in electronic microsystems makes the ever-increasing heat flux problem more serious. In this study, a highly efficient integrated single-phase microchannel cooler with four heat sources is presented for handling the challenges from both workings independently of all electronic modules and the high heat flux. Both numerical and experimental studies are conducted. By optimizing the structural design and the fabricated process, the presented microchannel cooler has outstanding cooling performance, which contains desired fluid flow distribution, pressure drop, heat transfer, and combination thereof. Results reveal uniform coolant flow dissipates four individual heaters independently, and their maximal temperature difference below 4 °C. Beyond this, high heat flux removal (707.6 W/cm2) is realized with an extremely low coolant flowrate (45 ml/min), and the maximum temperature rise is less than 60 °C. This study provides a referable solution for the thermal management of multi-module heat sources and high heat flux in compact electronic microsystems.