Nanofibrillated cellulose paper (nanopaper) has gained growing interest as one promising substrate material for paper-based microfluidics, thanks to its ultrasmooth surface, high optical transparency, uniform nanofiber matrix with nanoscale porosity, and tunable chemical properties. Recently, research on nanopaper-based microfluidics has quickly advanced; however, the current technique of patterning microchannels on nanopaper (i.e., 3D printing, spray coating, or manual cutting and sticking), that is fundamental for application development, still has some limitations, such as ease-of-contamination, and more importantly, only enabling millimeter-scale channels. This paper reports a facile process that leverages the simple operations of microembossing with the convenient plastic micro-molds, for the first time, patterning nanopaper microchannels downing to 200 μm, which is 4 times better than the existing methods and is time-saving (<45 mins). We also optimized the patterning parameters and provided one quick look-up table as the guideline for application developments. As proof-of-concept, we first demonstrated two fundamental microfluidic devices on nanopaper, the laminar-mixer and droplet generator, and two functional nanopaper-based analytical devices (NanoPADs) for glucose and Rhodamine B (RhB) sensing based on optical colorimetry and surface-enhanced Raman spectroscopy, respectively. The two NanoPADs showed outstanding performance with low limits of detection (2 mM for glucose and 19fM for RhB), which are 1.25× and 500× fold improvement compared to the previously reported values. This can be attributed to our newly developed highly accurate microchannel patterning process that enables high integration and fine-tunability of the NanoPADs along with the superior optical properties of nanopaper.