Nanoparticle-laden two-phase flow systems, especially atmospheric aerosols, are usually found with several modes for particle size distribution (PSD). For the first time, a mathematical method is proposed to study the interaction of nanoparticle dynamics between modes by establishing two joint population balance equations (PBEs). e PBEs are solved using the sectional method, which divides the PSD into discrete bins. e nanoparticle-laden system involves Brownian coagulation, ventilation, and injection. e interaction between modes within a size distribution is studied quantitatively with and without injection and ventilation. e study shows that particles with smaller size are easier to be removed by background particles, but the lag time to be removed is affected by not only the total number concentration of small particles but also their sizes. Background particles play an important role in determining the evolution of small particle system, whose presence makes the secondary model absent for the small particles.