The photochromic materials have been widely applied in many fields. In this article, we report a class of photochromic ammoniums with a dithienylethene backbone. They were utilized as templates to construct mechanically interlocked rotaxanes and pseudorotaxanes showing photo-responsive behavior by template-directed clipping reaction and the threading approach. The structures of novel rotaxanes were well defined. It is worth mentioning that the single crystal structure of [3]rotaxane containing two N-hetero crown ether units was obtained. Their photoisomerization behavior was investigated. These N-hetero crown ether-based rotaxanes displayed good reversibility and similar photochromic behaviors to their corresponding ammoniums when they underwent UV/vis photoirradiation. Interestingly, the cucurbit[6]uril-based pseudorotaxane showed better photoisomerization than its corresponding ammonium and those of N-hetero crown ether-based rotaxanes.