The self-diffusiophoresis of Janus catalytic micromotors (JCMs) in confined environment is studied using direct numerical simulations. The simulations revealed that, on average, the translocation of a JCM through a short pore is moderately slowed down by the confinement. This slowdown is far weaker compared to the transport of particles through similar pores driven by forces induced by external means or passive diffusiophoresis. Pairing of two JCMs facilitates the translocation of the one JCM entering the pore first but slows down the second JCM. Depending on its initial orientation, a JCM near the entrance of a pore can exhibit different rotational motion, which determines whether it can enter the pore. Once a JCM enters a narrow pore, it can execute a self-alignment process after which it becomes fully aligned with the pore axis and moves to the center line of the pore. Analysis of these results showed that, in addition to hydrodynamic effect, the translation and rotation of JCM is also affected by the “chemical effects”, i.e., the modification of the chemical species concentration around a JCM by confining walls and neighboring JCMs. These chemical effects are unique to the self-diffusiophoresis of JCMs and should be considered in design and operations of JCMs in confined environment.