This study demonstrated that excess Ca²⁺ increased the toxicity of Hg²⁺ to PSII of cyanobacterium Synechocystis sp. using fast rise chlorophyll fluorescence test. Excess Ca²⁺ increased the inhibitory effect of Hg²⁺ on O₂ evolution. Exposure to Hg²⁺ caused increase in functional antenna size (ABS/RC), trapping rate of reaction center (TR₀/RC), dissipated energy flux per reaction center (DI₀/RC) and maximum quantum yield of non-photochemical deexcitation (φDo), indicating that some reaction centers were transformed to dissipation sinks under Hg²⁺ stress. Hg²⁺ stress slowed down electron transport on both donor side and acceptor side and caused accumulation of P₆₈₀⁺. Excess Ca²⁺ intensified all the Hg²⁺ toxic effects on PSII function and led to dysfunction of PSII. The number of reaction centers that were transformed into dissipation sinks increased with increasing Ca²⁺ concentration.