Abstract: Quantum entities in the microscopic world possess wave-particle duality. However, for condensed matter systems composed of a large number of electrons and atomic nuclei, the Born-Oppenheimer approximation has conventionally been adopted over the past century as the first step in predicting or understanding physical problems. The central feature of this paradigm is that electrons exhibit wave-like behavior, while atomic nuclei are treated classically as particles. This article attempts to go beyond this conventional view under the approximation. We first introduce the full quantum effects beyond the Born-Oppenheimer approximation, focusing on nuclear quantum effects—which are partially accounted for by the approximation but are progressively weakened in practical treatments—and nonadiabatic effects, which are not considered by the approximation itself. Finally, taking the complex system of water/ice as an example, we explore new physical phenomena discovered from describing the lightest hydrogen nucleus (the proton) at the atomic scale via a wavefunction. This article emphasizes that the microscopic world is not simply a“scaled-down”version of the macroscopic world, nor vice versa.