Multifunctional mesoporous silica nanoparticles (MSNs) can confer dynamically varied release kinetics depending on the intermolecular interactions between model drugs and functional decorations on the MSNs. Herein, brush-like fluorescent conjugates were grafted on the pore walls of pristine MSNs for high drug loading and to impart fluorescence properties. The fluorescent MSNs (FMSNs) were further coated with polydopamine (PDA) and graphene oxide (GO) double layer, designated FMSNs@PDA and FMSNs@PDA@GO, respectively. The FMSNs@PDA@GO exhibited highly consistent drug release over one week (∼7 days) because of the consolidated PDA/GO double layer at neutral pH (7.4). However, the release rate of FMSN-Ibu@PDA@GO was increased at acidic pH (5.5) because the PDA/GO double layer was partially disrupted due to weakened π-π stacking and electrostatic interactions. The release kinetics of the FMSNs-based NPs (FMSNs, FMSNs@PDA, and FMSNs@PDA@GO) were systematically investigated using negatively charged hydrophobic ibuprofen and neutral hydrophilic acetaminophen at pH 7.4. In the FMSN-drug system, the release rate of acetaminophen was higher than that of ibuprofen because of the higher solubility of acetaminophen in aqueous solution. In addition, ibuprofen has a bulky molecular structure compared to acetaminophen, leading to its slower transmission through the porous channels of FMSNs. In the FMSNs-drug@PDA system, acetaminophen exhibited a slower release rate than ibuprofen, owing to the π-π stacking interactions in the transmission of neutral acetaminophen by the PDA coating layer. On the other hand, the FMSNs-drug@PDA@GO exhibited a slower ibuprofen release rate than acetaminophen, owing to the electrostatic repulsion effect of the negative GO layer. Our drug delivery system was demonstrated as an advanced delivery platform, in which the transmission rate is controlled by intermolecular interactions between the diffusing drugs and functional decorations on the nanocarrier.