Mg²⁺ plays important roles in many physiological processes. However, the underlying molecular mechanisms, especially in the apoptotic pathway, remain unclear due to the diffusion of Mg²⁺ probes, which hinders long-term imaging in specific organelles. We developed an immobilized Mg²⁺ probe, MGH, which is covalently conjugated with the HaloTag protein in various organelles. HaloTag-coupled MGH enabled long-term imaging of intracellular local Mg²⁺ dynamics for 24 h. To exploit this remarkable property, MGH was applied to the investigation of intracellular Mg²⁺ dynamics during apoptosis. Time-lapse imaging revealed an increase in the Mg²⁺ concentration after apoptotic cell shrinkage. Combined imaging analyses of intracellular Mg²⁺ and ATP concentrations strongly suggested that this Mg²⁺ concentration increase was caused by the dissociation of Mg²⁺ from ATP, along with a decrease in the intracellular ATP concentration. Thus, this protein-coupled Mg²⁺ probe could be a new chemical tool to elucidate intracellular Mg²⁺ dynamics with high spatiotemporal resolution.