Understanding the influence of the inner shell on fluorescence blinking and exciton dynamics is essential to promote the optical performances of InP-based quantum dots (QDs). Here, the fluorescence blinking, exciton dynamics, second-order correlation function g2(τ), and ultrafast carrier dynamics of InP/ZnSe/ZnS QDs regulated by the inner ZnSe shell thickness varying from 2 to 7 monolayers (MLs) were systematically investigated. With an inner ZnSe shell thickness of 5 MLs, the photoluminescence quantum yield (PL QY) can reach 98% due to the suppressed blinking and increased probability of multiphoton emission. The exciton dynamics of InP/ZnSe/ZnS QDs with different inner shells indicates that two decay components of neural excitons and charged trions are competitive to affect the photon emission behavior. The probability density distributions of the ON and OFF state duration in the blinking traces demonstrate an effective manipulation of the inner ZnSe shell in the non-radiative processes via defect passivation. Accordingly, the radiative recombination dominates the exciton deactivation and the non-radiative Auger recombination rate is remarkably reduced, leading to a QY close to unity and a high PL stability for InP/ZnSe/ZnS QDs with 5 MLs of the ZnSe shell. These results provide insights into the photophysical mechanism of InP-based QDs and are significant for developing novel semiconductor PL core/shell QDs.