Surface engineering of polymeric membranes can induce subtle changes in membrane properties and enhance their performance. Numerous membrane surface modification methods have been developed to improve the material performance. However, these methods can be complex, thus limiting their practical applications. Herein, we present a simple method for fabricating membranes with honeycomb surfaces by controlling the polymer molecular weight (Mw). Spirobisindane-based intrinsically microporous poly(ether-ether-ketone) (iPEEK-SBI) homopolymers with low and high Mws were synthesized and used to prepare organic solvent nanofiltration (OSN) membranes. The significant effects of polymer Mw on its physical properties, membrane morphology, and OSN performance were systematically investigated. iPEEK showed excellent solution processability, high Brunauer–Emmett–Teller surface area, and remarkable thermal stability. Three mechanically flexible OSN membranes exhibiting honeycomb surfaces with different honeycomb cell sizes were prepared using iPEEK-SBI homopolymers with low Mws at concentrations of 27–39 wt% in N-methyl-2-pyrrolidone. By contrast, the use of iPEEK-SBI homopolymers with high Mws yielded membranes with flat surfaces. The Mw cutoffs of the membranes were fine-tuned in the range of 408–772 g mol−1 by adjusting the dope solution concentration. Although the Mw cutoffs were unaffected by polymer Mw, the membranes derived from the polymer with low Mw exhibited substantially higher solvent permeance (18%–26%) than that of the high Mw membrane prepared at the same dope solution concentration. Stable performance was demonstrated over seven days of continuous cross-flow filtration and a six-month aging of the membranes. This work shows the importance of surface engineering for OSN membranes by adjusting polymer Mw. These findings open a new avenue for fine-tuning the properties of OSN membranes.