The affinity of partially hydrophobic silica nanoparticles for organic solvents (ethanol and hexane) was characterized using changes in relaxation time obtained from time-domain nuclear magnetic resonance (TD-NMR). Different chain lengths (C3, C6, and C12) were used as surface modifiers for the particles, with the modification ratio controlled. For ethanol, longer chain lengths and higher modification ratios resulted in higher affinity. Conversely, for hexane, the affinity was generally poor under all conditions, but shorter chain lengths and lower modification ratios showed higher affinity. We hypothesize that ethanol molecules are attracted to residual silanol groups among long-chain length functional groups. To test this hypothesis, we investigated the affinity of the partially hydrophobic silica nanoparticles in an ethanol/hexane mixture. In the range of 60 to 80 vol% hexane, the relaxation time of the C12-modified silica nanoparticles (with a modification ratio of 1.4/nm²) quickly decreased. This decrease disappeared when the residual silanol was additionally modified with C3. TD-NMR has proven to be an effective tool for detecting changes in surface affinity of partially hydrophobic nanoparticles, even when they exhibit the same hydrophobicity.