Cooling methods for multiple heat sources with high heat flux have rarely been reported, but such situations threaten the stable operation of electronic devices. Therefore, in this paper, the use of two microchannel heat sinks is proposed, with and without grooves, labeled Type A and Type B, respectively. Experimental investigations on the flow boiling of two microchannel heat sinks connected in parallel and in series are carried out under different mass fluxes. In addition, a high-speed camera is used to observe flow patterns in the microchannels. The cold plate wall temperature (Tw), heat transfer coefficient (HTC), and pressure drop (PD) are obtained with the use of two microchannel heat sinks. The flow patterns of the bubbly flow and elongated bubbles in the microchannels are observed. The results of the analysis indicated that the Tw, HTC, and PD of the two microchannel heat sinks connected in parallel were degraded, especially when using the Type A-B parallel connection. Compared to the use of a single heat sink, the maximum decrease in HTC was 9.44 kW/(m2K) for Type A heat sinks connected in parallel, which represents a decrease of 45.95%. The influence of the series connection on the Tw, HTC, and PD of the two heat sinks is obvious. The Type A-A series connection exerted the greatest positive effect on the performance of the two heat sinks, especially in the case of the postposition heat sink. The maximum increase in HTC was 12.77 kW/(m2K) for the postposition Type A heat sink, representing an increase of 72.88%. These results could provide a reference for a two-phase flow-cooling complex for multiple heat sources with high heat flux.