Particle morphology can affect the performance of an electrostatic precipitator air–liquid interface (ESP-ALI) cell exposure system and the resulting cell toxicity. In this study, three types of monodisperse aerosols–spherical sucrose particles, nonspherical align soot aggregates, and nanosilver aggregates/agglomerates–were selected to evaluate the collection efficiency at flow rates ranging from 0.3 to 1.5 lpm. To quantify the particle morphology, the fractal dimensions (Df) of the tested aerosols were characterized. The penetration of fine particles (dp = 100–250nm) under different operating conditions was correlated with a characteristic exponential curve using the dimensionless drift velocity (Vc/Vavg,r) as the scaling parameter. For nanoparticles (NPs, dp <100nm) with different particle morphologies, the particle penetrations in the ESP-ALI were similar, but their diffusion losses were not negligible. In contrast, for fine particles, the collection efficiency of soot nanoaggregates (Df = 2.29) was higher than that of spherical sucrose particles. This difference might be due to the simultaneous influences of the electric field-induced and flow field-induced alignment. Furthermore, based on Zhibin and Guoquan’s Deutsch model, a quadratic equation was applied to fit the experimental data and to predict the performance of the ESP-ALI.