The shrinking size of integrated chips poses thermal management challenges. Understanding the size effect of chemical heterogeneity on solid–liquid interfacial thermal transfer is essential for heterogeneous chip design, yet the underlying mechanisms remain lacking. The present work used the liquid n-alkanes as the thermal interface material between solid platinum substrates. To characterize chemical heterogeneity, periodic solid surface patterns composed of patches with alternating solid–liquid affinities were constructed. By using non-equilibrium molecular dynamics simulations, we investigated the size effect of chemically heterogeneous patterns on interfacial thermal resistance (ITR) at the nanoscale. At larger heterogeneity sizes, i.e., larger patch sizes, most alkane molecules directly in contact weak interaction patches cannot interact with strong interaction patches due to long atomic distances. In the case of alkanes in contact a cold substrate, alkanes in contact weak interaction patches transferred thermal energy to the substrate at a lower rate than those in contact strong interaction patches. The different rates resulted in the higher temperature of alkanes in contact weak interaction patches than those in contact strong interaction patches and, therefore, a larger disparity between temperature jump at the strong interaction areas and that at the weak interaction areas. The non-uniformity of temperature jump distribution increased ITR when compared to the heterogeneous surface system characterized by a smaller patch size with a more uniform temperature distribution in the plane perpendicular to the heat flux direction. In addition, the classical parallel thermal resistance model predicted ITR accurately for the heterogeneous surface systems with small size patches but overestimated overall thermal resistance.