Polyethylenimine (PEI)-DNA nanoparticles (NPs) have shown a lot of potential in gene delivery. The N/P ratio, the ratio between the total number of amines in PEIs and total number of phosphates in DNAs, is an essential factor determining the efficacy of delivery. In this work, the aggregation of PEIs and DNAs under different N/P ratios is studied using large-scale coarse-grained simulations under the Martini framework. At very low N/P ratio, the aggregation of DNAs is limited, and as the N/P ratio increases, the NPs change from a loose linear structure to a compact branched structure. Such a transition in the mode of aggregation is caused by the different alignments of PEIs with DNA backbones prior to aggregation, which dictates their ability to serve as polycation bridges. Except for very large NPs at high N/P ratios, the charge of a NP is proportional to the number of DNAs in it. Their ratio allows for the definition of an intrinsic property called specific repulsion, which controls the characteristics of the steady-state size distribution of NPs: unimodal for strong specific repulsion, bimodal for moderate specific repulsion, and more or less uniform for weak specific repulsion. Understanding the mechanism behind DNA-PEI NP formation helped us propose a two-step process to generate NPs that are more compact and closer to being spherical.