NASCION-type lithium-aluminum-germanium-phosphate (LAGP) glass-ceramic is one of the most promising solid electrolyte (SEs) material for the next generation Li-ion battery. Based on the crystallization of glass-ceramic material, the two-step heat treatment was designed to control the crystallization of Li-ion conducting crystal in the glass matrix. The results show that the LAGP crystal is preferred to internally crystalize, Tg + 60%∆T is the nucleation temperature that provides the highest ion conductivity. The compositional investigation also found that, pure LAGP crystal phase can be synthesized by lowering the amount of GeO2. To fill gap of atomic structure in LAGP glass-ceramic, molecular dynamic (MD) simulation was used to build the crystal, glass, and interfacial structure LAGP. The aliovalent ion substitution induced an simultaneously redistribution of Li to the 36f interstitial site, and the rapid cooperative motion between the Li-ions at 36f can drop the activation energy of LAGP crystal by decreasing the relaxation energy; furthermore, an energy model was built based on the time-based analysis of Li-ion diffusion to articulate the behavior. The glass and interfacial structure show and accumulation of AlO4, GeO4 and Li at the interface, which explains the Li-trapping on the intergranular glass phase. An in-situ synchrotron X-ray study found that, by using two-step heat treatment, the nucleation of Li-ion conducting crystal in the glass-matrix induced large strain from interfacial tension, which can also promote the incorporation of aliovalent ion substitution in the NASICON crystal and enhances the ion conductivity.