Synthesis of hierarchically porous structures with uniform spatial gradient and structure reinforcement effect still remains a great challenge. Herein, we report the synthesis of zeolite@mesoporous silica core-shell nanospheres (ZeoA@MesoS) with a gradient porous structure through a micellar dynamic assembly strategy. In this case, we find that the size of composite micelles can be dynamically changed with the increase of swelling agents, which in situ act as the building blocks for the modular assembly of gradient mesostructures. The ZeoA@MesoS nanospheres are highly dispersed in solvents with uniform micropores in the inner core and a gradient tubular mesopore shell. As a nanoreactor, such hierarchically gradient porous structures enable the capillary-directed fast mass transfer from the solutions to inner active sites. As a result, the ZeoA@MesoS catalysts deliver a fabulous catalytic yield of ∼75% on the esterification of long-chain carboxylic palmitic acids and high stability even toward water interference, which can be well trapped by the ZeoA core, pushing forward the chemical equilibrium. Moreover, a very remarkable catalytic conversion on the C-H arylation reaction of large N-methylindole is achieved (∼98%) by a Pd-immobilized ZeoA@MesoS catalyst. The water tolerance feature gives a notable enhancement of 26% in catalytic yield compared to the Pd-dendritic mesoporous silica without the zeolite core.