The electronic industry’s shift towards multicore processor technology which leads to an increase the power densities of the chip. In multicore processors the hotpot location arises depending on the computational load which leads to the generating the non-uniform heat flux. The uneven cooling of a multicore processor will affect the reliability and life span of the chip. In this study, employed parallel microchannel cooling systems (PMCHS) with different flow configurations by numerical simulations. The objective of the present work is to investigate the thermos-hydrodynamic characteristics of a PMCHS under a non-uniform heat load, the heat load is considered from an actively running 8-core processor. Here, considered that three types different flow configurations (U, I and Z) to determine the flow maldistribution, in additions the thermal performance of each flow configuration was analysed at non-uniform heat conditions. The size and shape of the PMCHS is equal to the octa-core processor which has been mimicked, and real-time heat load data of the processor has been retrieved. The present study exhibits that non-uniform thermal load creates additional non-uniform temperature distribution along with flow maldistribution in the PMCHS. Each flow configuration has a different flow maldistribution pattern, whereas the sometimes intended flow maldistribution helps to give better uniform cooling on the chip.