Stringent particulate emission regulations have been recently applied to spark-ignition direct-injection (SIDI) engine, calling for significant in-cylinder reduction of soot particles. These mandatory standards will be tall orders without understanding the soot formation and oxidation process within the flame. To bridge this gap, the present study a new thermophoresis-based sampling system has been developed and implemented in a working SIDI engine. Using the multiple probes installed on the piston top, the soot particles are directly sampled from the petrol flame for a close investigation on soot morphology. At the probe tip, a transmission electron microscope (TEM) grid is stored for the soot collection, which is imaged and post-processed for statistical analysis of particle size distribution and fractal dimension. Of particular interest is how the number of injection cycle, cyclic variation and sampling location impact the in-flame soot morphology at fixed engine operating conditions. To this end, the engine runs of 3, 5 and 7 injection cycles and other 6 sampling runs with fixed 5 injections were tested. The sampling experiment was also performed with the probes installed at four different locations on the piston top. Simultaneously, the flame development was recorded using two high-speed cameras to evidence the direct exposure of the sampling grids to the soot-laden diffusion flames and pool fires. The results show minor impact of injection cycle number on soot morphology. However, the size of soot primary particles and aggregates was found to increase with higher peak in-cylinder pressure and faster combustion speed associated with cyclic variations. Also, significant variations in morphology were observed for the soot particles sampled at four locations such that soot primary particles and aggregates are larger for the location where intensive pool fire develops.