In the present era, the elimination of hazardous dyes from wastewater has emerged as a paramount concern, captivating the interest of scientists globally because their detrimental effect on human health. Adsorption, a well-established and effective separation process, is commonly employed for eliminating various harmful organic pollutants from water, particularly toxic dyes. In this study, a novel magnetic organo-composite was synthesized through an environmentally friendly and easily implementable approach. Subsequently, various analytical techniques, including XRD, FT-IR, SEM, and EDX, were utilized to scrutinize the structure and morphology of the adsorbent. The as-prepared adsorbent demonstrated remarkable efficiency in rapidly removing malachite green dye from aqueous solutions, attaining a peak adsorption capacity of 227.40 mg g−1. Furthermore, several factors affecting the adsorption process were investigated, including adsorbent dosage, medium pH, initial dye concentration, and contact time. The examination of adsorption kinetics data indicated that the process adhered to a pseudo-second-order model (R2 = 0.97), implying that chemisorption constituted the controlling step in the reaction. Additionally, the experimental adsorption isotherms exhibited a close fit to the Langmuir model (R2 = 0.98). Crucially, the SDS/CTAB/Fe3O4@Sep magnetic organo-nanocomposite adsorbent exhibited the capacity for multiple reuses, maintaining its effectiveness over five cycles without notable activity decline. Consequently, the synthesized organo-composite appears to show potential as an effective adsorbent for eliminating harmful cationic dyes present in wastewater. Molecular dynamics (MD) simulations, employing Monte Carlo adsorption locator simulation (MCL) calculations, further supported the elevated adsorption of SDS/CTAB on Sep, Fe3O4 on SDS/CTAB@Sep, and MG molecules on SDS/CTAB/Fe3O4@Sep due to their negative adsorptions.