MIL-53(Fe) was synthesized using a “modulator approach” that utilizes acetic acid (HAc) as an additive to control the size and morphology of the resulting crystals. We demonstrate that after activation under vaccum at 100 °C, the MIL-53(Fe) functions well for H2S selective oxidation. The introduction of acetic acid in the presence of benzene-1,4-dicarboxylic acid (H2BDC) would result in a series of MIL-53(Fe) nanocrystals (denoted as MIL-53(Fe)-xH, x stands for the volume of added HAc with morphology evoluting from irregular particles to short hexagonal columns. The vacuum treatment facilitates the removal of acetate groups, thus generating Fe3+ Lewis acid sites. Consequently, the resulted MIL-53(Fe)-xH exhibits good catalytic activity (98% H2S conversion and 92% sulfur selectivity) at moderate reaction temperatures (100–190 °C). The MIL-53(Fe)-5H is superior to the traditional iron-based catalysts, showing stable performance in a test period of 55 h.