The esterification of cyclohexene with formic acid is the first step for indirect hydration to cyclohexanol. In the work reported in this study, phosphotungstic acid (HPW) was incorporated into the metal-organic framework Cu-3(BTC)(2) through a one-step hydrothermal synthesis method to catalyze the esterification reaction. The crystal structure of composite HPW-Cu-3(BTC)(2) was modulated during the preparation process to convert the catalyst from the {111} crystal facets of the original regular octahedral structure to the {100} crystal facets of the cubic structure using p-toluic acid (pTA) as the regulator. The conversion of the crystal facets reduces the formation through holes while exposing more active sites of HPW. When the mass ratio of the modulator to the organic ligand terephthalic acid was 20, the crystal facets of the catalyst were completely covered by the {100} crystal facets. After the crystal transformation, the conversion of cyclohexene was increased to 86.8%, and the selectivity of cyclohexyl formate was 84.2%. Agglomeration occurred after the catalyst was used twice in the esterification reaction. Graphic HPW was incorporated into the metal-organic framework Cu-3(BTC)(2) through a one-step hydrothermal synthesis method and used for catalyzing the esterification reaction of cyclohexene with formic acid. The crystal structure of composite HPW-Cu-3(BTC)(2) was modulated during the preparation process to convert the catalyst from the {111} crystal facets of the original regular octahedral structure to the {100} crystal facets of the cubic structure using p-toluic acid (pTA) as the modulator.