The present disclosure discloses an alignment system and an alignment method for a container or vehicle inspection system, and an inspection system. The inspection system comprises comprising an ray source, a collimator, a detector arm and a detector module mounted on a detector arm, the ray source, the collimator and the detector module are arranged to form an inspection passage, a ray beam emitted from the ray source passes through collimator and irradiates onto an inspected object, and an attenuated ray beam is collected by the detector module so as to complete inspection. The alignment system comprises a measuring module arranged to receive the ray beam emitted from the collimator and to measure the ray beam so as to determine positions and orientations of the ray source and the collimator. With the alignment method, alignment between a center point of the ray source, a central line of a detector tip and a central line of the collimator may be more accurately measured.