Heparin, usually isolated from porcine intestinal mucosa, is an active pharmaceutical ingredient of great material value. Traditionally, diverse types of commercial resins were employed as an adsorbent for heparin retrieval from biological samples. However, more recent years have encouraged the advent of new cost-effective adsorbents to achieve enhanced heparin retrieval. Inexpensive cationic ammonium-functionalized silica gels, monodispersed with larger surface area, porosity, and higher thermal stability, were chosen to evaluate the heparin recovery yield from porcine intestinal mucosa. We demonstrated that higher positively charged and less bulky quaternary modified silica gel (e.g., QDASi) could adsorb ~28% (14.7 mg g−1) heparin from the real samples. In addition, we also determined suitable surface conditions for the heparin molecule adsorption by mechanistic studies and optimized different variables, such as pH, temperature, etc., to improve the heparin adsorption. This is going to be the first reported study on the usage of quaternary amine-functionalized silica gel for HEP uptake.