In view of the high sensitivity and good selectivity, chemical vapor generation atomic spectrometry (CVG-AS) and inductively coupled plasma mass spectrometer (ICP-MS), especially low-cost atomic fluorescence spectrometry (AFS) have been widely used in bioassay. However, the existing AS method is mostly based on heterogeneous strategies, and can't detect multiple targets in one system. In this study, we present the discovery and mechanism study of a phenomenon of Hg2+ pre-reduction that the concentration of Hg2+ decreased when it was mixed with the reductants (ascorbic acid (AA), SnCl2, or NaBH4/KBH4) over long-time reaction (hours) by CVG-AFS and ICP-MS. A homogeneous Cu2+ assay method was developed based on the competition reaction of Cu2+ and Hg2+ for consuming AA, and its application in the detection of pyrophosphate (PPi) and alkaline phosphatase (ALP) was investigated based on the PPi complexation with Cu2+, and ALP hydrolyzation of PPi using CVG-AFS as a representative detector. Subsequently, in order to further verify the applicability of the system, cation exchange reaction (CER) was utilized here based on the selectively recognize Ag+ and C–Ag+-C by CuS nanoparticles (NPs). As the exchanged Cu2+ from CuS NPs can be sensitively and selectively detected via above-mentioned Cu2+ assay method, this strategy can be extended for the Ag+, DNA and prostate specific antigen (PSA) detection based on base complementary pairing and the specific recognition of aptamer. Under the optimal experimental conditions, the system showed high sensitivity for the detection of Cu2+, PPi, ALP, Ag+, DNA, and PSA, with limit of detections (LODs) of 0.12 nmol L−1, 25 μmol L−1, 0.025 U/L, 0.2 nmol L−1, 0.05 nmol L−1, and 0.03 ng/mL, respectively. The method was successfully used to determination Cu2+, ALP, and PSA in human serums, showing similar results with those of ICP-MS and kits methods.