TiO2-ZrO2-(3,5-di-tert-butylcatechol, DTBC) composite membranes were fabricated via the sol–gel method under four different firing conditions: 300 °C (N2), 300 °C (Air), 350 °C (Air), and 500 °C (Air). The chemical structure of the DTBC originated organic material in the composite was controlled by setting the firing temperature. The average pore sizes of the membranes were 1.0–1.1 nm when fired at 300 °C, 1.4 nm at 350 °C, and 2.1 nm at 500 °C. The molecular weight cut-off of the membranes (in daltons) in water ranged from 480 to 535 when fired at 300 °C, 890 at 350 °C, and 1,680 at 500 °C, whose corresponding molecular diameter was in good agreement with the average pore size measured via nanopermporometery. Permeation tests of the organic solvents showed that the membrane-solvent interaction affected the permeation mechanism in addition to the solvent viscosity and the occupied area of the solvent molecules. The surface free energy difference between the membrane and the solvent expressed the interaction between the membrane and the solvent molecule. The proposed solvent permeation model was examined and showed better agreement with the experimental results compared with the model based on the solubility parameters of a solvent. The organic solvent permeation mechanism of the ceramic NF membrane was greatly affected by the membrane-solvent intermolecular interaction.