Membrane-based pervaporation (PV) is highly efficient and energy-saving, and is poised to emerge as a promising technology for recovering biofuels from aqueous solutions. In this study, we prepared two versions of zeolite membranes, randomly oriented and highly (h0h)-oriented silicalite-1, with similar thicknesses on α-alumina tubes, and performed the first-reported systematic comparison of their PV performances in recovering organic solvents such as methanol, ethanol, acetone, n-propanol, isopropanol, and n-butanol from water. The contribution of the intrinsic properties of these membranes to PV was explored through permeance and selectivity analysis. The highly (h0h)-oriented membrane exhibited a significantly higher level of PV performance. In addition, the permeation behavior of PV and single-gas molecules through the highly (h0h)-oriented membranes was investigated, along with the influence that operating conditions (feed temperature and concentration) exert on PV. The results suggest that the PV permeation mechanism of organic solvent/water systems through the (h0h)-oriented silicalite-1 membranes involves a combination of adsorption-diffusion and molecular sieving. Furthermore, compared with other MFI-based membranes reported in the literature, the highly (h0h)-oriented silicalite-1 membrane demonstrated outstanding comprehensive separation performance due to its highly hydrophobic, preferentially oriented, and uniform silicalite-1 layer. For example, the separation factors for 10 wt% binary aqueous solutions of methanol, ethanol, acetone, and n-propanol were 12 at 50 °C, 32 at 70 °C, 145 at 70 °C, and 37.7 at 50 °C, respectively, with corresponding total flux values of 4.18, 2.63, 2.5, and 0.29 kg/(m2 h), respectively. These unique properties suggest its potential for PV recovery of organic solvents in sustainable chemical engineering.