In gold ore, quartz plays an important role in mineral formation by acting as the follower. Understanding counterion release, transport, and deposition in alkali solution is a prerequisite for evaluating the potential role of gold separate from quartz deposits in pretreatment. In this work, the aggregation, retention, and release of counterion in alkali solution media were investigated by kinetic research and pure mineral experiments, the correlation and mechanism of these processes were revealed by combining geochemical theory, interaction energy calculation, and quantum chemistry. The results showed that the retention and release of counterion were closely related to the dissolution and corrosion rate of quartz. The NH4+ and Fe2+ with higher mineral affinity reduced the quartz stability, and the dispersion stability and mobility of the quartz were greatly improved by an alkaline substance due to the enhancement of steric hindrance effects. Quantum chemical calculation results show that ammonium ion promotes the dissolution of quartz stronger than ferrous ion, which is mainly reflected in reducing the activation energy required for the formation of transition state (TS1), which can be verified by kinetic calculation. These findings provide essential insight into the extraction of gold coated by quartz as well as a vital reference for the experiment of gold-loaded quartz leaching in mineral processing.