The biological early warning system with fish behavior as the detection index is an efficient and rapid early warning technology for the ecological damage caused by water pollutants. However, the attempt to apply the scototaxis (dark preference) behavior of fish to biological early warning is still relatively lacking. In this study, we delved into the dark and light preferences of the rare minnows (Gobiocypris rarus), employing three distinct tank configurations. Additionally, we systematically examined the modulating effects of environmental illumination, nutritional status, and the number of test subjects on this behavior, aiming to establish optimal experimental parameters for its observation. Furthermore, cadmium ions [Cd2+], tricaine methanesulfonate [MS222], and p-chloroaniline were employed as representative heavy metal ions, neuroactive agents, and organic toxicants, respectively, to test the impact of chemicals on scototaxis in gradient concentrations. The results demonstrated that the rare minnow exhibited a clear scototaxis (dark preference), and this behavior was not affected by the nutritional status of the test fish, the illumination, or the number of subjects. While the dark chamber was consistently the preferred location of rare minnows during the chemical exposure tests, the degree of scototaxis by the rare minnow significantly decreased at Cd2+ ≥ 3 mg/L, MS222 ≥ 11 mg/L, and p-chloroaniline ≥ 29 mg/L, suggesting a potential disruption of their innate behavioral patterns by these chemicals. These findings underscore the sensitivity of rare minnows to water pollutants. Therefore, the scototaxis behavior of rare minnows can be a potential and useful behavioral indicator for biological early warning, which can be used for early biological warning of sudden water pollution caused by chemicals such as Cd2+, MS222, and p-chloroaniline.