The invention discloses a construction process of a double-layer jacking culvert penetrating through existing railway lines. The construction process includes the following steps: (1) precasting of an upper-layer bridge culvert body, (2) construction of a back and a back beam used for jacking of the upper-layer bridge culvert body, (3) reinforcement of the existing railway lines, wherein the existing railway lines are reinforced through a line overhead reinforcing structure, (4) digging of a jacking pit of the upper-layer bridge culvert body, (5) jacking of the upper-layer bridge culvert body, (6) construction of a bottom supporting system of the upper-layer bridge culvert body, (7) detachment of the line overhead reinforcing structure, (8) precasting of a lower-layer bridge culvert body, (9) construction of a back and a back beam used for jacking of the lower-layer bridge culvert body, (10) digging of a jacking pit of the lower-layer bridge culver body, (11) jacking of the lower-layer bridge culvert body, and (12) concrete pouring, wherein after the lower-layer bridge culvert body is jacked properly, concrete is poured between the upper-layer bridge culvert body and the lower-layer bridge culvert body. The method is simple, reasonable in design, low in investment construction cost and good in using effect, the construction process of the double-layer jacking culvert can be easily, conveniently and quickly finished and is high in quality, and the construction process is safe and reliable.