A series of novel five coordinated mercury(II) complexes of a new recently synthesized tridentate ligand are presented. The mercury(II) complexes were characterized by various spectral and physical techniques such as FTIR, UV–visible, 1H and 13C NMR spectra, thermal analyses, and decomposition temperature and conductivity measurement. Also nanostructure size of titled mercury coordination compounds have been prepared by the reaction of ligand and mercury salts under ultrasonic conditions. The nanostructure size of the complexes was confirmed by XRD patterns, scanning electron microscopy, and transmission electron microscopy. According to the mentioned analyses, the molecular formula of HgLX2 (X = halide and/or pseudo-halide anions and L = ligand) was suggested for the complexes. Thereafter all mercury(II) complexes were tested for their in vitro antibacterial activities against two Gram-positive (Staphylococcus aureus and Bacillus subtilis) and two Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacterial strains. Also in vitro antifungal activities of them against Candida albicans and Aspergillus niger were investigated. The results indicated that all compounds can act as antibacterial and antifungal agents. Moreover, thermal behaviors of the complexes were studied in the range of 20–900 °C. Thermogravimetric study indicated that the mercury complexes are thermally degraded via 3–9 thermal steps.