The dynamics and the conditions of amorphous transitions induced in a GeSb2Te4 system upon a single 108 fs pulse melting were studied by real-time optical microscope measurements. The system has a multilayer structure of 100 nm ZnS-SiO2/35 nm GeSb2Te4 /120 nm ZnS–SiO2/0.6 mm polycarbonate substrate. The amorphization is completed within 2.6 ns. The thickness of the phase change layer plays an important role in controlling the heat flow conditions in the system upon a fs pulse irradiation. The relative thermal process and effects are analyzed. The mechanism of crystalline to amorphous transition triggered by single femtosecond laser pulses is discussed.