Some soot particles emitted from common-rail diesel engines are so small that can penetrate deep into the human pulmonary system, causing serious health issues. The analysis of nano-scale internal structure of these soot particles sampled from the engine tailpipe has provided useful information about their reactivity and toxicity. However, the variations of carbon fringe structures during complex soot formation/oxidation processes occurring inside the engine cylinder are not fully understood. To fill this gap, this paper presents experimental methods for direct sampling and nanostructure analysis of in-flame soot particles in a working diesel engine. The soot particles are collected onto a lacey carbon-coated grid and then imaged in a high-resolution transmission electron microscope (HR-TEM). The HR-TEM images are post-processed using a Matlab-based code to obtain key nanostructure parameters such as carbon fringe length, fringe-to-fringe separation distance, and fringe tortuosity. Of particular interest is how jet-jet interactions impact the soot nanostructures because a wall-jet head merging with a neighbouring jet head is well known to cause high soot formation due to rich mixtures. The soot sampling was conducted for three different jet configurations including two single jets (Jet A and Jet B) and a double jet (Jet A&B). Results show that soot primary particles from all the jet configurations are comprised of two distinctively different structures of multiple amorphous cores and concentrically-oriented carbon-layer shells. From about 5000 carbon fringes processed for each jet configuration, the Jet A and Jet B samples show nearly identical mean values for the fringe length, separation distance, and fringe tortuosity of 0.955∼0.962 nm, 0.398∼0.399 nm, and 1.22, respectively. This suggests that jet-to-jet (or hole-to-hole) variations make a minimal impact on the soot nanostructures. The Jet A&B sample also displays similar tortuosity; however, 4% higher fringe separation distance (0.415 nm), which is well outside of the error range, and the increased proportion of highly reactive short carbon fringes suggest that soot particles formed in the jet-jet interaction region are more pre-mature and reactive than those formed in the single-jet head region.