As one of the most successful nonvolatile phase change materials (PCMs), Ge2Sb2Te5 (GST) can be reversibly switched between amorphous and crystalline phases by nanosecond laser pulses, which enables its applications in optical disks and various emerging reconfigurable photonic devices. Instead of simply inducing temperature rising of GST thin film via light absorption, high-energy laser irradiation leads to modifications of molecular bonds, forming different local structures. We employed a nanosecond pulse laser with different pulse duration, energy and pulse numbers to induce multi-level switching of GST thin films. By employing Raman spectroscopy, we illustrated that GeTe4–nGen (n = 0, 1, 2) subsystem plays a decisive role in laser-induced crystallization of GST. Different from isothermal annealing, where SbmTe3 (m = 1, 2) subsystem contributes as well. This is evidenced by the suppression of SbmTe3 structure of an isothermally annealed film treated with additional laser crystallization. In addition, our investigations indicated that in GeTe4–nGen subsystem, Joule heating promotes the formation of Te-rich tetrahedral components. These findings provide more insights into the structural characteristics of GST.