Studying and controlling the risk factors of shield tunnel crossing underneath the adjacent existing subway tunnel will be of great significance for guaranteeing the safety of tunnel structure. Under the background of subway undercrossing engineering in Shenzhen, 3D finite element models under different working conditions were established using the theory of orthogonal experimental design. The disturbing impacts generated by newly built tunnel shield crossing beneath the existing tunnel to the existing tunnel were explored in consideration of different factors. Based on the impact degrees of different experimental indexes, the priority and weight of each index were determined via the analyses of range and variance in the orthogonal experiment. The results show that the clear distance and spatial angle between new and old tunnels, and soil chamber pressure exert highly significant impacts on the settlement of the existing tunnel structure; the maximum tensile stress of the existing tunnel structure is significantly impacted by the clear distance, spacing, thickness of overburden layer, and angle; the settlement value of the existing tunnel is extremely sensitive to the soil chamber pressure, with the impact weight reaching 24.9%, and the maximum tensile stress of the existing tunnel is sensitive to the change in the thickness of overburden layer: With the increase in the thickness of overburden layer, the maximum tensile stress presents a significant trend of progressive increase, and the impact weight reaches 19.25%. The study results will be of reference significance to the safety construction of shield tunnel crossing beneath the adjacent existing subway tunnel.