Perylene diimide and its derivatives are promising photocatalysts for clean and efficient production, but their practical application in the field of photocatalysis is still limited by the rapid photogenerated charge recombination. In this work, the confined photocatalysts were synthesized by using a gas-phase self-assembly method and comparing the morphology and photocatalytic properties of different photocatalysts after the confinement of carbon nanotubes. The confinement effect of carbon nanotubes acts to stabilize perylene diimide. Electrostatic interaction formed by a wide range of dispersion forces is dominant in the process of stabilization. Benefitting from the three-dimensional electron transfer pathway formed by the conjugation of perylene diimide with a large number of π electrons to the carbon nanotubes plane, the confined photocatalyst shows the pseudo-first-order kinetic constant k of 1.106 h−1 for the photocatalytic degradation of diclofenac under light, which is 6.11 times higher than that of perylene diimide. The electron transfer created an internal electric field at the interface from carbon nanotubes to perylene diimide, which greatly accelerated the separation of photogenerated electron-hole pairs and improved the photocatalytic activity. This study further expands the applicability of perylene diimide in the field of photocatalysis and provides a new approach for water environment treatment.