Mercury, a highly toxic metal and pollutant, poses a significant risk to human health and the environment. This study describes the synthesis of a new nitrogen-doped heteroaromatic hyper-crosslinked polyamine (HCPA) via the polycondensation of 2,6-diaminopyrazine and tris(4-formylphenyl)amine for the efficient removal of mercury ions from aqueous solutions. The HCPA polymer was characterized by solid-state ¹³C-NMR and FT-IR spectroscopy. A powder X-ray diffraction and thermogravimetric analysis showed that the polymer was semicrystalline in nature and stable up to 500 °C. Adsorption isotherms indicated that mercury adsorption occurred via mono- and multilayer adsorption by HCPA, as depicted by the Langmuir, Freundlich, and Redlich–Peterson isotherm models, with a maximum adsorption capacity of q_m = 333.3 mg/g. Adsorption kinetic models suggested that the adsorption process was fast and effective, reaching equilibrium within 20 min. Thermodynamics of the adsorption process revealed that it was endothermic and spontaneous in nature due to the positive ΔH⁰ of 48 kJ/mol and negative ΔG⁰ values of −4.5 kJ/mol at 293 K. Wastewater treatment revealed 98% removal of mercury indicating the selective nature of HCPA. Finally, HCPA exhibited excellent performance and regeneration up to three cycles, demonstrating its great potential as an adsorbent for environmental remediation applications.