The objective of this study was to elucidate the cooperative modification mechanism of anionic composite pharmaceuticals on coal substrates. Composite pharmaceuticals were synthesized using sodium hexametaphosphate (SHMP) and sodium polycarboxylate to reduce coal hygroscopicity. The mesoscopic alteration process between the coal surfaces and the compound pharmaceuticals was examined via atomic force microscopy (AFM). AFM showed that SHMP was multilayer-adsorbed on coal via electrostatic and hydrogen bonding, while sodium polycarboxylate was single layer-adsorbed at the SHMP layer via electrostatic interactions. Composite pharmaceutical adhesion to coal was lower than that for individual pharmaceuticals, indicating synergistic effects. The mechanism underpinning the microscopic synergistic effect of complex pharmaceuticals on the coal surface was further examined using density functional theory (DFT) at the molecular scale. DFT calculations showed that the adsorption energy of SHMP binding to a sodium polycarboxylate molecule was greater than that of SHMP binding to two identical pharmaceutical molecules. The SHMP portion generally interacted with the aromatic coal nucleus via its ring structure, exposing the sodium polycarboxylate carbon chain to maximize the adsorption energy. Combining DFT and AFM provided insight into the composite pharmaceutical function, and a theoretical framework for coal flotation separation was established.