Understanding the electrical double layer (EDL) structure at the solid/liquid interface is critical towards realizing the full potential of electrochemical applications using ionic liquids. In this work, the out-of-plane and in-plane EDL structures of PYR14-TFSI on graphite (HOPG) have been studied by in-situ electrochemical atomic force microscopy (AFM) and molecular dynamics (MD) simulation. AFM results revealed that the first adsorbed ion layer on HOPG consists of both disordered and ordered lateral domains. It has been found that the neighboring molecules in the x-y plane form intricate ordered lateral structures on length scale of hundreds of nanometers, and the out-of-plane EDL structure is independent of the in-plane structure. MD simulations under zero polarization showed that in the first adsorbed layer, cations have one preferred orientation while anions have two preferred orientations in relation to the HOPG surface, which might be the origin of the complex lateral ordering. When polarizing the surface, a hysteretic order-disorder transition of the lateral ordering in the first adsorbed layer can be observed by in-situ AFM, and the ordered domains disappear for high positive or negative voltages. Comparison with bias-dependent MD reveals that the existence of a bimodal anion distribution in the first absorbed layer can be linked to the observed transitions giving new insights into the origin of the structural domains, which can help understand unusual charge and discharge kinetics observed in similar systems.