The Ti-based metal-organic framework (Ti-MOF) MIL-125 with tunable crystalline size in the range of ca. 50 nm to 1500 nm was synthesized by the coordination modulation method using trans-cinnamic acid (CA) as a modulator. The coordination modulation also induced hierarchical porosity and structure defects on the nanocrystals. A significant size-dependent catalytic activity towards the oxidative desulfurization (ODS) reaction was observed for these MIL-125 nanocrystals. In particular, the MIL-125 nanocrystals with a mean size of ca. 50 nm exhibit dramatically enhanced catalytic performance for the bulky sulfur compound 4,6-dimethyldibenzothiophene (4,6-DMDBT) compared to the microcrystals. It is demonstrated that the size modulation of MIL-125 is an effective approach to promote its performance for the catalysis of bulky molecules.