The ladder-type benzimidazobenzophenanthroline (BBL) polymer is one of the most important and most studied n-type conducting polymers. It is also an organic mixed ion-electron conductor (OMIEC), which can undergo electrochemical switching in electrolyte solutions by accommodating opposite ions. The extensive morphological changes of the OMIEC material during operation affect the transport properties and, hence, the device performance. However, molecular insights into the dynamic structural changes during the electrochemical switching are limited, as they are difficult or impossible to access in experiments. The computational microscope based on molecular dynamics (MD) calculations can provide us with complete insights into the detailed dynamic morphological changes that are currently missing, to a large extent, for the BBL polymer. In the present study, using atomistic MD simulations, we obtained microscopic insights into the electrochemical switching of BBL film in two different electrolytes, namely, single-atom counterion K+ (potassium) in water and molecular counterion DMBI+ (dimethyl-3-butyl imidazolium) in chloroform. For both cases, the maximum crystallinity is found up to a moderate reduction level. Beyond that, ion intercalation initiates a structural phase transition and causes a decrease in the crystalline order of the film. At the higher reduction levels, the single-atom K+ counterions are stabilized within the lamellar stacked BBL chains; in contrast, the DMBI+ counterions with higher molecular weights are stabilized within the BBL pi-pi stacks, forming pi-pi stacking between BBL and DMBI+. Our findings substantiate how molecular dopants can improve the thermomechanical stability of the material and why smaller single-atom counterions are preferred for maintaining better crystallinity. The detailed microscopic insights into the morphological changes during the electrochemical switching of BBL film, which cannot be directly accessed experimentally, can definitely help design n-type OMIEC-based devices made of BBL.