Molecularly functional drug delivery systems possessed huge potentials to realize novel drug administration. To explore small molecules modified drug delivery, a series of small molecules modified mesoporous silica nanoparticles (L-Mal-MSNs, D-Mal-MSNs) were established by grafting small molecules. Poorly water-soluble indomethacin (IMC) was chosen to load into these small molecules modified carriers as well as corresponding control carrier, and further to study characteristics and delivery effects of drug loaded carriers. The results indicated that all these small molecules modified carriers formed hydrogen bonds with drugs and can successfully convert drug crystal phase to amorphous state so as to enhance drug dissolution compared to raw drug. In vivo rat intestinal perfusion demonstrated that IMC loaded L-Mal-MSNs performed the fastest drug absorption while analgesic and anti-inflammatory effects of IMC loaded D-Mal-MSNs turned out to be the best, giving hints that D-malic acid exhibited best synergic functions for IMC. The herein small molecules modified delivery system is an effective solution strategy for the current application of analgesia and anti-inflammatory drugs with outstanding significance.