The co-assembly of charged nanoparticles with oppositely charged molecular ions has emerged as a promising technique in the fabrication of nanoparticle superstructures. However, the underlying mechanism behind these molecular ions in mediating the repulsion between these charged nanoparticles remains elusive. Herein, coarse-grained molecular dynamics simulations are used to elucidate the effects of valency, shape and size of molecular anions on their co-assembly with gold nanoparticles coated with positively charged ligands. The findings suggest that the valency, shape and size of molecular anions significantly influence the repulsion and aggregating dynamics among these positively charged nanoparticles. Moreover, the free energy calculations reveal that ring-shaped molecular anions with higher valencies and larger sizes are more effective at reducing the repulsion between these gold nanoparticles and thus enhance the stability of the aggregate. This study contributes to a better understanding of the critical roles of valence, shape and size of ions in mediating the electrostatic co-assembly of nanoparticles with oppositely charged ions and it also guides the future design of DNA templates and DNA origami in co-assembly with oppositely charged nanoparticles.