In this study, mixed-mode chromatography columns have been investigated using multiple analyte interactions. A mixed-mode chromatography column was developed using poly(N-isopropylacrylamide) (PNIPAAm) brush-modified silica beads and poly(3-acrylamidopropyl trimethylammonium chloride) (PAPTAC) brush-modified silica beads. PNIPAAm brush-modified silica beads and PAPTAC brush-modified silica beads were prepared by atom transfer radical polymerization. The beads were then packed into a stainless-steel column in arbitrary compositions. The elution studies evaluated the column performance on hydrophobic, electrostatic, and therapeutic drug samples using steroids, adenosine nucleotide, and antiepileptic drugs as analytes, respectively. Steroids exhibited an increased retention time when the column temperature was increased. The retention of adenosine nucleotides increased with the increasing composition of the PAPTAC-modified beads in the column. The antiepileptic drugs were separated using the prepared mixed-mode columns. An effective separation of antiepileptic drugs was observed on a 10:1 PNIPAAm:PAPTAC column because the balance between the hydrophobic and electrostatic interactions with antiepileptic drugs was optimized for the bead composition. Oligonucleotides were also separated using mixed-mode columns through multiple hydrophobic and electrostatic interactions. These results demonstrate that the developed mixed-mode column can modulate multiple hydrophobic and electrostatic interactions by changing the column temperature and composition of the packed PNIPAAm and PAPTAC beads.