Self-engineered small-molecule prodrug-nanoassemblies have emerged as promising nanomedicines for cancer treatment. Modular design of prodrug molecules is crucial to guarantee the favorable assembly stability, tumor-specific prodrug activation, and satisfactory antitumor effect. However, too much attention has been paid to the pharmacophores and chemical linkages in prodrug molecules while neglects the vital roles of nonpharmacological moieties. Herein, we found that iso-carbon fatty acids with different number, position, and cis-trans configuration of double bonds dramatically affect the nanoassembly feature and drug delivery fates of thioether-linked paclitaxel prodrug-nanoassemblies. Particularly, the number and cis-trans configuration of double bonds in fatty acid moieties not only dominate the self-assembly ability and colloidal stability of prodrugs, but also exert significant influences on the pharmacokinetics, prodrug activation, and antitumor activity of prodrug-nanoassemblies. Finally, oleic acid with one cis double bond stands out as the optimal nonpharmacological moiety for thioether-linked paclitaxel prodrug-nanoassemblies. This study elucidates the crucial roles of nonpharmacological moieties in prodrugs, and provides new insights into the modular design of prodrug-based nanomedicines for cancer therapy.