Based on the laser controlled hot fracture method, a method of separating thick transparent materials with a multi-focus laser is proposed. The optical system which can support three focal points is designed by using the theoretical calculation and ZEMAX software simulation. The separation experiments of transparent materials including laminated glass, potassium dihydrogen phosphate (KDP) crystal and ultra clear glass are carried out by using this system. The results show that this method can obtain the flat and smooth cross section without sub-surface damage and with small roughness, which effectively solves the problem that the hot fracture separation method by a single laser focus is limited by the material thickness, and has great application prospects.