Nowadays, the controllable synthesis of stable hierarchical metal–organic frameworks (MOFs) is very important for practical applications, especially in catalysis. Herein, a well-known chromium–benzenedicarboxylate metal–organic framework, MIL-101(Cr), with a stable hierarchical structure, was produced by using phenylphosphonic acid (PPOA) as a modulator via the hydrothermal method. The presence of phenylphosphonic acid could create structural defects and generate larger mesopores. The synthesized hierarchical MIL-101(Cr) possesses relatively good porosity, and the larger mesopores had widths of 4–10 nm. The hierarchical MIL-101(Cr) showed significant improvement for catalytic activity in the oxidation of indene. Further, the presence of a hierarchical structure could largely enhance large dye molecule uptake properties by impregnating.