Pollution of water resources by various pollutants is a global environmental issue, particularly, dye pollution has a major contribution to it. From various studies, it is confirmed that adsorption is an excellent remediation technique compared to others. Mg–Al-layered double hydroxides (LDHs) intercalated with NO3– ions act as an effective adsorbent-removing ionic species like heavy metal and dyes. Another popular nanomaterial is graphene oxide (GO), which is successfully used as an adsorbent for different pollutants like dye and heavy metal ions. It is prepared based on the modified Hummers method. In this study, GO was introduced on the surface of LDH to improve its adsorption capacity. The adsorption process is well described by the Freundlich model. The maximum adsorption capacity was obtained at around 0.5 and 0.85 mmol of methylene blue (MB) per gram of Mg–Al LDH and modified Mg–Al LDH with GO, respectively. The reaction kinetics of MB with both adsorbents is determined to be the pseudo-second-order. To get more insights of the mechanism, molecular dynamics (MD) simulation was conducted among the modified Mg–Al LDH with GO and MB molecules at both low- and high-concentration environments, which demonstrated that the developed composite adsorbs MB molecules predominantly onto its GO surface and then the MB molecules are adsorbed by the LDH surface. C–H···O (2.49–3.04 Å) and pi-donor···H–O (2.45–3.05 Å) are the major driving forces behind the strong adsorbability. Besides, S···H–O, S···O,N···O–H, pi···lone pair, pi···sigma, pi···cation, and alkyl···hydrophobic interactions play important roles in stabilizing the MB molecules onto the surface of the composite.