By utilizing scanning tunneling microscopy (STM), the self-assembled nanostructures of three characteristic aldehydes have been examined at the solution-solid interface. By introducing the active reactant 5-aminoisophthalic acid (5-AIPA), we succeeded in changing the self-assembled molecular structures through the condensation reaction and obtained the information on structural transformation in real time. The corresponding carboxyl conjugated derivatives were formed in situ and developed into the closely packed and ordered molecular architectures via hydrogen bonds at the solution-solid surface. The relevant simulations have been utilized to interpret the mechanisms of forming the nanostructures. The corresponding theoretical calculation is used to explain the reaction mechanism. Compared with the traditional ways, the on-surface condensation reaction in situ could not only provide a more convenient method for regulating the self-assembled architectures but also offer a promising strategy for building functional nanostructures and devices.