Flow boiling in microchannels is one of the most effective ways to solve the heat dissipation problems caused by the aggressive miniaturization of electronic components. In this study, counter-flow stepped microchannels (CSMC) are designed to address the main issues currently faced by boiling two-phase flow in microchannels: premature triggered critical heat flux (CHF) and severe boiling instability. Flow boiling experiments are conducted in three CSMCs with different step depths of 100 μm, 200 μm, and 300 μm, respectively. Deionized water is used as the working fluid, and the mass flux ranges from 118 kg/m2·s to 370 kg/m2·s. Combined with the visualization results captured by a high-speed camera, the boiling heat transfer and instability characteristics in three CSMCs are investigated and compared with the traditional parallel-flow straight microchannels (PMC). The results show that the CHF and average heat transfer coefficient (HTC) of CSMCs are increased by 50.0%-105.6% and 35.8%-90.3%, respectively, while the two-phase pressure drop is decreased by 61.7%-77.7% compared to PMC. The design of the step structure can disrupt the boundary layer, change the flow velocity between different steps, and promote fluid mixing, all of which are more pronounced in the case of deeper step depth. Therefore, with the increase in step depth, the CHF and average HTC are increased, and the two-phase pressure drop decreases. More importantly, the flow boiling instability in CSMC is well suppressed. The oscillations of the wall temperatures are eliminated during the flow boiling process in CSMC. Compared with PMC, the magnitudes of pressure oscillations in CSMCs are decreased by 52.8%-84.9%, and the rises in inlet temperatures caused by flow reversal are also achieved in a 6.1 °C-36.6 °C reduction. Similarly, the suppression effect on boiling instability increases with the step depth. The visualization results revealed that for CSMC with the largest step depth, the upstream expansion of bubbles is not observed throughout the flow boiling experiment. All above encouraging results indicate that the demonstrated counter-flow stepped microchannels would provide a good reference for future microchannel design.