The identification and selective preference for different habitats is one of the important abilities to ensure the survival and reproduction of fish. The preference of Rare Minnow (Gobiocypris rarus) for different habitat and the effects of nutrient status, number of components and environmental illumination on this behavior were tested. Sand, aquatic plants, and stones were used in a variety of permutations and combinations in tank to create different habitat types. The behavior was quantified based on the time spent of fish in each area of tank and frequency of midline crossing. The effects of nutrient status, number of components and environmental illumination was tested under following condition respectively by the controlling the variable method: (1) Two groups of nutritional status of fish: food-deprived and well-fed. Fish of food-deprived was stopped feeding for 24 h; (2) Four groups of ambient illumination: 500 lx, 1 000 lx, 1 500 lx, 2 000 lx; (3) Four groups of number of components: one, two, four, eight aquatic plants. Data were checked for assumptions of normality and assumptions of homogeneity of variance by using Kolmogorov- Smirnov and Levene tests and were analyzed by One Way Analysis of Variance and least significant difference (multiple-comparison tests). Statistical process and tests were done using the SPSS and Office Excel. Results showed that Rare Minnow had obvious preference to different habitat types (P < 0.05), and this preference degree was highest when containing only aquatic plants, and was lowest when containing only rocks (Fig. 2 and Fig. 3). This preference was not affected after food-deprived of 24 h (P > 0.05, Fig. 5), but was significantly affected by the number of habitat components (P < 0.001, Fig. 4) and environmental illumination (P < 0.001). It increased with the increase of number of aquatic plants and illumination, and was most obvious when containing 8 aquatic plants (Fig. 4) or under the illumination of 1 000 lx (Fig. 6). In conclusion, this study demonstrates that Rare Minnow had obvious preference to environment composed of aquatic plants and this preference was affected significantly by some environmental factors such as illumination and number of habitat components.