For better understanding of in-cylinder soot formation processes and governing factors of the number of emitted soot particles of Gasoline Direct Injection (GDI) engines, Transmission Electron Microscope (TEM) analysis of morphology and nanostructure of the soot particles sampled in the exhaust should provide useful information. However, the number concentration of the soot particles emitted from GDI engines is relatively low, which was impeding reliable morphological analysis of the soot particles based on a sufficient number of sampled particles. Therefore, in the present study, a water-cooled thermophoretic sampler for simple and direct sampling of exhaust soot particles was developed and employed, which enabled to obtain a sufficient number of particle samples from the exhaust with Particulate Number (PN) 105 #/cc level for quantitative morphology analysis. Using the developed sampler, soot particles were sampled from the exhaust of a single-cylinder GDI test engine operated with three different fuel injection timings (advanced, normal, retarded) and their morphology and nanostructure were quantitatively analyzed. Number concentration and size distribution of the emitted particles were simultaneously measured with Scanning Mobility Particle Sizer (SMPS). The sampled GDI soot particles appeared to have typical chain-like aggregate structure and graphite-like inner-particle nanostructure similar to well-known diesel ones. The aggregate size (gyration radius) and the primary particle diameter ranged from 20 to 200nm and from 5 to 60nm, respectively, and both decreased depending on the fuel injection timing, in the order from advanced, normal and retarded. The distribution of TEM-based aggregate gyration diameter qualitatively well corresponded to that of SMPS-measured particle size, except that numerous nanoparticles smaller than 23nm, likely due to condensed volatile components detected by SMPS, but not observed in the TEM analysis.