As one of the pollutants that cannot be ignored, soot has a great impact on human health, environment, and energy conversion. In this investigation, the effect of residence time (25ms, 35ms, and 45ms) and ammonia on morphology and nanostructure of soot in laminar ethylene flames has been studied under atmospheric conditions and different flame heights (15 mm and 30 mm). The transmission electron microscopy (TEM) and high-resolution transmission electron microscope (HRTEM) are used to obtain morphology of aggregates and nanostructure of primary particles, respectively. In addition, to analyze the nanostructure of the particles, an analysis program is built based on MATLAB software, which is able to obtain the fringe separation distance, fringe length, and fringe tortuosity parameters of primary particles, and has been verified by the multilayer graphene interlayer distance. It is found that soot is mainly composed of tens of primary particles in the form of tree-like at HAB (height above burner) = 30 mm. But the primary particles are dispersed with the use of ammonia at HAB = 15 mm. Moreover, the mean diameter of primary particles is greatly affected by fuels and it is mainly distributed between 16 nm–36 nm. For ethylene flame, it increases first and then decreases with the increase of residence time. For the ethylene ammonia flame, it keeps rising. In addition, the mean fringe separation distance and fringe tortuosity are not affected by residence time. However, with the increase of residence time, the mean fringe length decreases first and then increases for ethylene flame, while for ethylene ammonia flame, the mean fringe length decreases. Furthermore, with the addition of ammonia, the mean separation distance decreases and the mean fringe length increases slightly.