Understanding the interactions between mercury and microalgae, especially the interactions between inorganic mercury (IHg) and extracellular polymeric substances (EPS, a protective barrier between cells and their external environment), is essential for elucidating mercury's toxicological mechanisms. Given the inherent cell heterogeneity, a novel analysis system of an online viscoelastic fluid focusing chip-time-resolved analysis inductively coupled plasma mass spectrometry has been developed to investigate the bioaccumulation of HgS nanoparticles and Hg2+ in single Microcystis aeruginosa (M. aeruginosa) cells, exploring the interaction mechanisms between HgS/Hg2+ accumulation in algal cells and EPS. The single-cell analysis results reveal minimal bioavailability of HgS within algal cells, with mercury's toxicity to M. aeruginosa being species-dependent. Notably, algal cells exhibited more heterogeneity in HgS uptake than in Hg2+ uptake. Under Hg2+/HgS stress, M. aeruginosa cells with EPS removed (EPS-R algal cells) showed an increased level of bioaccumulation of mercury compared to those with EPS (EPS-C algal cells), highlighting the critical role of EPS in mercury bioaccumulation. Overall, the designed viscoelastic fluid microfluidic focusing chip integrates focusing and cleaning functions, featuring easy fabrication, simple operation, low sample loss, and relatively high throughput. Under the optimal conditions, the sample throughput is 1195 min-1 and the cell recovery is 90%. Besides, this research offers novel insights into the interaction mechanisms between Hg2+/HgS and EPS in microalgal cells and unveils the specific toxic effects of Hg2+/HgS on M. aeruginosa at the single-cell level, contributing to a deeper understanding of mercury's ecological and toxicological impact in aquatic environments.