In this work, thermophoretic sampling experiments are carried out in a constant volume combustion chamber (CVCC) accompanied by the subsequent high-resolution transmission electron microscopy (HRTEM) imaging to investigate the morphology, nanostructure, and size of soot particles directly sampled within the reacting diesel jet spray flame under ambient conditions close to practical engine combustion. The experiments are performed with different fuel injection masses to examine the variation of the morphological and nanostructural parameters of soot primary particles and aggregates with the fuel injection quantity, Q(s) The results show the particles sampled in the cases with low fuel injection quantity (Q(s)) have a fraction of separately existing small primary particles and small aggregates made up of only several primary particles. As the fuel injection mass is further increased, the number of soot particles increase but the projection area becomes smaller. The fractal dimension of the sampled aggregates is found to increase from 1.66 to 1.86 with the fuel injection mass. The particles sampled under different Q(s) cases have similar sphericity (Phi) and circularity (C) values. Especially, no abrupt changes appear in the C and Phi values as the particle size increases. The correlation between C and 1 values reveals the small-size soot particles are more likely to show an ellipse shape, while the larger ones are more likely to exhibit irregular shapes, neither spherical nor chain-like. The normalized histograms of the diameter of primary particles exhibit a normal distribution pattern for all the fuel injection quantities tested. Larger primary particles and soot agglomerates are associated with the higher fuel injection quantiy. The HRTEM analysis indicates the fringe tortuosity and separation distance decrease as the fuel injection quantity increases, while the fringe length increases with increasing fuel injection quantity.