Multi-layer flexible PVC films used in this study were produced via the micro-layer co-extrusion technology and the influences of micro-layer co-extrusion technology on plasticizer migration of flexible PVC were investigated. It was shown that the morphology of PVC molecule chains changed from the coiled state into the linear ordered state. The linear alignment is more compact with evenly dispersed additives in the PVC matrix after micro-layer co-extrusion. The volatility stability, solvent extraction stability, exudation stability, and film tensile strength were tested. The results indicated that, films made by micro-layer co-extrusion technology showed excellent plasticizer migration stability and mechanical properties, due to the ordered PVC molecule chains and the even additive dispersion.