The inhibitory effect of Cr(VI) on the PSII of Synechocystis sp. was studied. Cr(VI) reduced O2 evolution and inhibited the water-splitting system in PSII. S-states test and flash induction test showed that Cr(VI) exposure increased the proportion of inactivated PSII (PSIIX) and PSIIβ reaction centers, which increased the fluxes of dissipated energy. JIP test and QA− reoxidation test demonstrated that Cr(VI) treatment induces inhibition of electron transport from QA− to QB/QB− and accumulation of P680+. More QA− had to be oxidized through S2(QAQB)− charge recombination and oxidation by PQ9 molecules in PSII under Cr(VI) stress. These changes finally decreased the index of photosynthesis performance.