Organic small molecular semiconductors have been promising candidates for the future electronic materials and devices, and their charge transport potentials have been expected to catch-up and surpass the benchmark one in Si - the giant in the semiconductor materials. As represented in the mobility values observed in graphene with μ > 10⁴ cm² V^-1 s^-1, the extended Π-conjugated electron systems provide highly conductive platforms for electrons and holes, however the charge transport in aggregates of conjugated small molecules is disturbed by inter-molecular thermal fluctuations, resulting in the lower mobility of charge carrierreffs in the molecular systems. We have developed a novel assessment technique of charge carrier mobility on the nanoscale molecular aggregates, referred to as time-resolved microwave conductivity (TRMC) measurement, where the non-contact approach minimizes the inter-aggregates issues in the conventional assessment techniques. Particularly, the combination of TRMC with transient absorption spectroscopy (TAS) realizes herein fully experimental non-contact measurement of mobility in supramolecular architectures without structural modulation of the archtectures in the device fabrication protocols. Electron mobility observed in one-dimensional naphthalenediimide (NDI) stacking structures was determined as μ_-,1D = 10^-3-10^-4 cm² V^-1 s^-1 based on the values of photoconductivity Δσ and photo-carrier generation yield φ determined by TRMC and TAS, respectively. The NDI stacked structures with a variety of inter-molecular interactions were systematically examined by the combined spectroscopy systems, revealing the remarkable impact of interactions stabilizing the stacking structures on the mobility values.