A wavefront aberration model with respect to substrate deformation error of membrane diffractive lens is built by means of diffractive ray tracing and wavefront reconstruction method. Two typical cases of the substrate deformation errors, the edge wrinkle surface and the spherical surface with center outward structure, are demonstrated. Meanwhile, the influence of the deformation errors on related image quality is evaluated and the principal aberration type caused by the deformation errors is discussed. The relationship between wavefront root-mean-square aberration, surface peak-to-valley value and Strehl ratio (SR) is investigated. This work would be helpful in assembling membrane diffractive lens and compensating aberration in a real diffractive telescope system.