Two functional main-chain linear polyrotaxanes, one a covalent polymeric chain that threads through many macrocycles (P1) and the other a poly[n]rotaxane chain that is composed of many repeating rotaxane units (P2), were synthesized by employing strong crown-ether/ammonium-based (DB24C8/DBA) host-guest interactions and click chemistry. Energy transfer between the wheel and axle units in both polyrotaxanes was used to provide insight into the conformational information of their resulting polyrotaxanes. Steady-state and time-resolved spectroscopy were performed to understand the conformation differences between polymers P1 and P2 in solution. Additional investigations by using dynamic/static light scattering and atomic force microscopy illustrated that polymer P1 was unbending and had a rigid rod-like structure, whilst polymer P2 was curved and flexible. This flexible topology facilitated the self-assembly of polymer P2 into relatively large ball-shaped particles. In addition, the energy transfer between the wheel and axle units was controlled by the addition of specific anions or base. The anion-induced energy enhancement was attributed to a change in electrostatic interactions between the polymer chains. The base-driven molecular shuttle broke the DB24C8/DBA host-guest interactions. These results confirm that both intra- and intermolecular electrostatic interactions are crucial for modulating conformational topology, which determines the assembly of polyrotaxanes in solution.