The deformation and failure mechanism of cylindrical shells and square plate with pre-formed holes under blast loading were investigated numerically by employing the Ansys 17.0 and Ls-Dyna 971. To calibrate the numerical model, the experiments of square plates with pre-formed circle holes were modeled and the numerical results have a good agreement with the experiment data. The calibrated numerical model was used to study the deformation and failure mechanism of cylindrical shells with pre-formed circle holes subjected to blast loading. The structure response and stress field changing process has been divided into four specific stages and the deformation mechanism has been discussed systematically. The local and global deformation curves, degree of damage, change of stress status and failure modes of cylindrical shell and square plate with pre-formed circular holes are obtained, compared and analyzed, it can be concluded as: (1) The transition of tensile stress fields is due to the geometrical characteristic of pre-formed holes and cylindrical shell with arch configuration; (2) The existence of pre-formed holes not only lead to the increasing of stress concentration around the holes, but also release the stress concentration during whole response process; (3) There are three and two kinds of failure modes for square plate and cylindrical shell with pre-formed holes, respectively. and the standoff distance has a key influence on the forming location of the crack initiating point and the locus of crack propagation; (4) The square plate with pre-formed holes has a better performance than cylindrical shell on blast-resistant capability at a smaller standoff distance, while the influence of pre-formed holes on the reduction of blast-resistant capability of square plate is bigger than that of cylindrical shell.