Semiconductor quantum dots (QDs) exhibit unique optical and photophysical properties that offer significant advantages over organic dyes as optical labels for chemo/bio-sensing. This review addresses the methods for metal ion detection with QDs, including photoluminescent, electrochemiluminescent, photoelectrochemical, and electrochemical approaches. The main mechanisms of direct interaction between QDs and metal ions which lead to photoluminescence being either off or on, are discussed in detail. These direct interactions provide great opportunities for developing simple yet effect metal ion probes. Different methods to design the chemically-modified QD hybrid structures through anchoring metal ion-specific groups onto the surface of QDs are summarized. Due to the spatial separation of the luminescence center and analyte recognition sites, these chemically-modified QDs offer greatly improved sensitivity and selectivity for metal ions. Several interesting applications of QD-based metal ion probes are presented, with specific emphasis on cellular probes, coding probes and sensing with logic gate operations.