Affinity between partially hydrophobic silica nanoparticles and organic solvents (ethanol and hexane) as dispersing medium has been characterized with change in the relaxation time obtained by a time-domain nuclear magnetic resonance (TD-NMR). Different chain lengths (denoted as C3, C6, and C12) were utilized as surface modifiers for the particles and the modification ratio was controlled. For ethanol, the longer chain length and higher modification ratio showed the higher affinity while for hexane, vice versa even though a quite poor affinity appeared in whole conditions. We hypothesize that the ethanol molecules could be attracted to residual silanol groups among long-chain length-functional groups. In order to prove, affinity of the partially hydrophobic silica nanoparticles with ethanol/hexane mixture has been investigated. In the range from 60 to 80 vol% of hexane, relaxation time of the C12-modified silica nanoparticles (modification ratio was 1.4 /nm2) quickly decreased. When the residual silanol was additionally modified with C3, the corresponding decrease disappeared. The TD-NMR has an effective tool to detect the change in the surface affinity of the partially hydrophobic nanoparticles even if they showed the same hydrophobicity.