Flow boiling in microchannel evaporators is widely recognized and promising for its compact structure, lower coolant usage, high heat transfer coefficient, ability to provide higher heat fluxes, and better temperature uniformity than single-phase liquid cooling. However, critical heat flux (CHF), local dry-outs, and flow instabilities can be significant roadblocks for practical implementation. Flow instabilities, like pressure drop oscillation, could lead to nonuniform wall temperature distribution, flow reversal, and local dryout, which can be detrimental to system performance. We conducted an experimental study of a vapor compression cycle incorporating a microchannel evaporator to investigate the role of evaporator design and various system parameters on the overall performance. These parameters include the expansion valve setting, the accumulator heat load, and the evaporator heat load. While the evaporator design, the testbed, and system parameters affect the system response in unique ways, flow instability can be explained based on the overall pressure drop occurring in the system and how it varies as a function of these factors. Based on the understanding gained from this experimental study, a dynamic control strategy was developed to stabilize the system facing transient heat loads. The system can successfully address transient evaporator heat loads with feedforward control, which would otherwise lead to pressure drop oscillation. We believe this study can be helpful in further development of active control techniques to achieve multiple objectives of maintaining fixed evaporator temperature, allowing higher cooling rates, avoiding CHF, and suppressing flow instabilities, even in the presence of transient heat loads.