The invention discloses pyridinium ion modified near infrared squaric acid dye as well as a preparation method and application thereof. Pyridinium ion modified trimethyl dihydroindole derivatives anddicyanovinyl square acid derivatives are used as raw materials to prepare the near infrared squaric acid dye. The near infrared squaric acid dye has high stability and excellent optical performance; particularly pyridinium ion groups can enhance the dye water solubility; when the near infrared squaric acid dye is used for aquacide detection, aquacide molecules and dye molecules can mutually act, so that the absorption spectrum and fluorescence spectrum change can be caused, so that the materials can be used as fluorescence probes for aquacide detection, can be used for aquacide fluorescence detection in the environment, and has higher detection sensitivity.