Zeolite nanoparticles have been widely used to overcome diffusion limitations in heterogeneous catalytic reactions. However, the existence of surface barriers for molecular diffusion in zeolites can limit the benefits of using nanoparticles in catalytic reactions. In this study, a set of silica nanoparticle (SNP)/silicalite-1 composites with different external surface to micropore surface ratios was synthesized to understand the effects of surface-controlled mass transport on molecular diffusion in zeolite nanoparticles. The zero length column (ZLC) technique was used to evaluate the mass transport of cyclohexane in these materials. It was found that the strong sorbate/sorbent interaction at the external surface of silicalite-1 nanoparticles can cause diffusing molecules to re-enter into micropores and repeat the micropore diffusion process. This pore re-entry step can lead to an unusually long micropore diffusion length. We also demonstrated that this repeated micropore diffusion process can be effectively reduced by mixing the zeolite nanoparticles with secondary, nonporous nanoparticles. This study provides an alternative way to justify the surface mass transfer resistance, and it also introduces a simple strategy to enhance mass transport in zeolite nanoparticles other than surface modification which can damage the integrity of zeolite crystals. Additionally, previous diffusion results were revisited by adjusting the actual micropore diffusion length. It was concluded that the surface resistance in zeolite nanoparticles is likely due to a combination of pore re-entry of adsorbates and pore blockage.