In this study, by decorating the chromenylium-cyanine structure with an indoline ring, a new sensor platform CSI with a highly rigid structure and improved photophysical properties was developed for the first time. The CSI platform was modified with glyoxal and L-methionine methyl ester to produce a new NIR, ratiometric, and switch-on probe (CIME). This probe is biocompatible, water soluble, and has a specific binding mode for Hg2+ ion selectivity. The crystal structure of CSI was determined by x-ray crystallography, and its electronic characteristics, including HOMO-LUMO energy levels were determined by quantum mechanical calculations. CIME is the first instance of an indoline-fused chromenylium-cyanine used for quantification of trace level of Hg2+ in both the living cells and the environment. The new probe has a high level of selectivity and sensitivity for Hg2+ in aqueous media, with broad linear ranges (0–300 μM for UV-Vis and 0–225 μM for fluorescence). It has a rapid response time of 30 seconds, and UV-Vis and fluorescence detection limits of 7.4 ng/mL and 0.13 ng/mL, respectively. Probe quantitatively detected Hg2+ in real samples using UV-Vis, fluorescence spectrophotometry and a smartphone. The interaction between CIME and Hg2+ was verified by FTIR, HRMS and DFT calculations. Furthermore, the ability of CIME to sense Hg2+ in living cells was confirmed in both MCF-7 cells and 3T3 cells.