Singlet oxygen as an activated oxygen species played an important role in organic synthesis. Suitable catalyst for converting ubiquitous oxygen molecule to singlet oxygen under mild conditions has attracted a wide range of attention. Herein, carbon dots have been confined into mesopores of silicalite-1 nanocrystals framework and acted as active sites for generation of singlet oxygen. The high oxygen-adsorption capacity of zeolite nanocrystals facilitated the photocatalytic generation rate of singlet oxygen, outpacing the free-standing carbon dots for 14-fold. The integrated carbon dot-zeolite nanocrystal hybrid also exhibited a special size-dependent selectivity for organic synthesis by using the in situ formed and confined singlet oxygen as active oxygen species.