Silicon-based microfluidic devices, so-called micromodels in this application, are particularly useful laboratory tools for the direct visualization of fluid flow revealing pore-scale mechanisms controlling flow and transport phenomena in natural porous media. Current microfluidic devices with uniform etched depths, however, are limited when representing complex geometries such as the multiple-scale pore sizes common in carbonate rocks. In this study, we successfully developed optimized sequential photolithography to etch micropores (1.5 to 21 μm width) less deeply than the depth of wider macropores (>21 μm width) to improve the structural realism of an existing single-depth micromodel with a carbonate-derived pore structure. Surface profilimetry illustrates the configuration of the dual-depth dual-porosity micromodel and is used to estimate the corresponding pore volume change for the dual-depth micromodel compared to the equivalent uniform- or single-depth model. The flow characteristics of the dual-depth dual-porosity micromodel were characterized using micro-particle image velocimetry (μ-PIV), relative permeability measurements, and pore-scale observations during imbibition and drainage processes. The μ-PIV technique provides insights into the fluid dynamics within microfluidic channels and relevant fluid velocities controlled predominantly by changes in etching depth. In addition, the reduction of end-point relative permeability for both oil and water in the new dual-depth dual-porosity micromodel compared to the equivalent single-depth micromodel implies more realistic capillary forces occurring in the new dual-depth micromodel. Throughout the imbibition and drainage experiments, the flow behaviors of single- and dual-depth micromodels are further differentiated using direct visualization of the trapped non-wetting phase and the preferential mobilization of the wetting phase in the dual-depth micromodel. The visual observations agree with the relative permeability results. These findings indicate that dual-porosity and dual-depth micromodels have enhanced physical realism that is pertinent to oil recovery processes in complex porous media.