Performance tests on caffeine’s corrosion inhibition properties and their derivatives against copper corrosion have been previously reported experimentally using gravimetric and electrochemical analyses. The test was able to measure the efficiency of their corrosion inhibition accurately. However, the caffeine and its derivatives’ structure patterns and coating mechanisms when interacting with metals during copper corrosion inhibition have not been explained in detail by experimental studies. In the present study, the theoretical density functional study (DFT), ab initio MP2, and Monte Carlo simulation approaches explain the problem. The geometrical and quantum chemical parameters of inhibitors were compared under normal and protonated conditions in the gas and aqueous environments. Theoretical studies can accurately determine the molecule’s geometrical parameters and successfully explain the quantum parameters of inhibitors. Molecular dynamics are applied to study the mechanism of interaction between inhibitors and metal surfaces in an explicit water molecule environment. The energy absorption of caffeine and its derivatives on metal surfaces was linear, with quantum parameters calculated from the density functional theory and an ab initio approach. Furthermore, these theoretical study results align with the previously reported experimental studies published by de Souza et al. The inhibition efficiency ranking of studied molecules preventing copper corrosion was caffeine > theobromine > theophylline. This theoretical approach is expected to bridge the gap in designing effective corrosion inhibitors.