The lack of an ideal silicone-based ink material with optimal printability has significantly limited the potential to fabricate silicone-based microfluidic devices via 3D vat photopolymerization (VPP) printing. Oftentimes, photoabsorbers are incorporated into the ink material for better control of the photocuring depth in order to avoid excessive curing of unwanted parts. However, the search for a suitable photoabsorber without staining the ink material remains challenging due to the need to retain the clear interface in the final printed product. Herein, we present the fabrication of highly precise and transparent microfluidic devices using hydrophilic silicone-based ink via 3D VPP printing upon photocuring depth adjustment with cellulose nanocrystals (CNC). With the optimal CNC content, the ink material demonstrates enhanced printing accuracy with highly precise replication of channel patterns consisting of near zero deviation in width dimension down to 100 µm. Moreover, the addition of optimal CNC content exhibits no distinct final color and has no negative impact on the pre-gel viscosity and the gel point of the developed ink material. Moving on, the printed devices exhibit excellent fluid manipulation with various solvents for up to 24 hours, with incubation temperature up to 100ºC for 5 hours, and with a continuous flow rate up to 20 mL/min. The sustainable hydrophilicity, good organic solvent resistance, and excellent biocompatibility properties of the printed material further eliminate the need for additional surface modification to suit its application with either organic solvents or biological cells. To the best of our knowledge, the approach to tuning the photocuring depth of ink material with CNC is not widely reported. Besides, the successful fabrication of a highly detailed, neutral-colored, and highly functional hydrophilic silicone-based microfluidic device via 3D VPP printing upon the incorporation of CNC introduces a new avenue in terms of printing material and fabrication method for the mass production of microfluidic devices.