This research delved into the influence of mesoporous silica’s surface charge density on the adsorption of Cu²⁺. The synthesis of mesoporous silica employed the hydrothermal method, with pore size controlled by varying the length of trimethylammonium bromide (C_nTAB, n = 12, 14, 16) chains. Gas adsorption techniques and transmission electron microscopy characterized the mesoporous silica structure. Surface charge densities of the mesoporous silica were determined through potentiometric titration, while surface hydroxyl densities were assessed using the thermogravimetric method. Subsequently, batch adsorption experiments were conducted to study the adsorption of Cu²⁺ in mesoporous silica, and the process was comprehensively analyzed using Atomic absorption spectrometry (AAS), Fourier transform infrared (FTIR), and L3 edge X-ray absorption near edge structure (XANES). The research findings suggest a positive correlation between the pore size of mesoporous silica, its surface charge density, and the adsorption capacity for Cu²⁺. More specifically, as the pore size increases within the 3–4.1 nm range, the surface charge density and the adsorption capacity for Cu²⁺ also increase. Our findings provide valuable insights into the relationship between the physicochemical properties of mesoporous silica and the adsorption behavior of Cu²⁺, offering potential applications in areas such as environmental remediation and catalysis.