Habitat selection by Hynobius maoershanensis was performed during the reproductive period in Maoershan Natural Reserve in Guangxi, including Peak Lake, Three Rivers, and Savage Lake. Sixty-one plots were randomly set up, with egg bags for the selected plots and no egg bags for the control plots, to survey 20 types of habitat factors (e.g., temperature and humidity, vegetation type, vegetation coverage, water area, water depth, water type, bottom sand ratio, and human disturbance). (1) The results of 6 descriptive ecological factors revealed significant differences among 3 factors (shore condition, water cover, and water body) for selecting quadrats and control plots and no significant differences in the other 3 ecological factors (vegetation type, degree of human disturbance, and egg bag suspension). (2) The results of 9 factors with abnormal distribution showed that vegetation coverage, water-sediment ratio, water flow rate, and water area were significantly different between the selected quadrats and control plots, indicating that H. maoershanensis favored lower vegetation cover, lower water sediment, lower water velocity, and larger water body area to lay eggs. (3) The stepwise discrimination of 14 numerical ecological factors showed that the correct discrimination rate for the selected quadrats and control plots by vegetation coverage (largest contribution, 0.840) and sediment concentration (second largest contribution, 0.622) was 80.3%. (4) Stepwise regression analysis of the number of egg bags and 14 types of ecological factors showed a significant positive correlation between the selected habitat and surface humidity for H. maoershanensis and a significant negative correlation with vegetation cover. The high surface humidity and low vegetation coverage promoted the spawning capacity of H. maoershanensis. In conclusion, the micro-habitat preferred by H. maoershanensis is a hydrostatic pond with low water velocity, low vegetation coverage, large amount of water cover, relatively low sediment concentration, complex shore condition, and large water area, which act as the main factors for habitat selection during the breeding period of H. maoershanensis.