Position deviation of joints is a primary initial geometrical imperfection that affects the stability of long-span spatial structures. It makes field measurement of joint coordinate for the shell and roof initial shape of Nantong Sports Exhibition Center upon its completion. This paper researches the stochastic distribution feature and statistical parameter of geometrical imperfections for the data sources of above position deviation of joints by “abnormal data test method”. The results indicate that the distribution of abnormal data is concentrated, which is related to the difficulty of construction and condition of measurement; the distribution of joint position deviation can be assumed by normal distribution, and its mean μ=0 and mean square deviation σ=R/2 of statistical parameter are tenable. Meanwhile, It also puts forward a stochastic imperfection method based on measured imperfections and ANSYS－PDS platform, establishes a measured model to make nonlinear stability analysis, and respectively compares this critical load with that obtained by the perfect structure of ideal shape and the consistent imperfection method, so as to evaluate the stability and reliability of practical project in an objective manner, and provide reference for project design.