The highly efficient production of furfuryl alcohol (FFA) from biomass-derived furfural (FFR) is attracting increasing attention due to its wide application in the production of value-added chemicals. Zr-based MOF-808 is promising for liquid catalytic transfer hydrogenation (CTH) of FFR to FFA in terms of possessing a great number of Lewis-acid sites. Herein, a series of defective MOF-808 (Dx-MOF-808) samples were prepared via a competitive coordination-removal strategy by modulating with benzoic acid (HBC). HBC was introduced as the temporary ligand for competing with formal ligand 1,3,5-benzenetricarboxylic acid (H3BTC) to coordinate with metal clusters and then it was removed with methanol to obtain the Dx-MOF-808. The results showed that HBC serves not only as a temporary ligand participating in the synthesis of MOF-808 to obtain defective structure but also as a modulator controlling the particle size by terminating the growth of crystals. By changing the amount of HBC addition, the degree of ligand deficiency and the number of exposed Zr sites can be well regulated. Especially, excellent performance of FFR conversion (99%), FFA selectivity (94.4%) and FFA formation rate (48.6 mmol·g−1·h−1) was achieved over D40-MOF-808 sample with 2-propanol as a hydrogen donor under mild conditions (90 °C, 2 h), ranking it the best among the reported catalysts. Detailed characterizations proved that the high activity of D40-MOF-808 was jointly influenced by the high surface area, the high content of exposed Zr metal sites and ligand deficiency.