Concrete cracks often appear in construction period and operation period of the canal lining. For analyzing the cause of these cracks, the factors which will cause cracks are classified based on the data collected. Also sensitivity analysis on these factors is carried out with 3D contact nonlinear finite element method. The result shows that, the factors which resulting in concrete cracks are temperature variation, humidity, uneven settlement of foundation, expansion deformation of foundation soil, external loads etc.; Joint-cutting should be done as soon as possible, expansive property of the foundation soil and construction quality of canal lining should be strictly controlled.