Atmospheric conditions have non-negligible impacts on middle-school student travel. This paper aims to compare and explore the effect of atmospheric conditions on middle-school students’ travel mode choices in Beijing based on generalized additive mixed models (GAMM). Many atmospheric conditions, including temperature, humidity, and air pollutants, were found to have significant nonlinear effects on middle-school students’ travel mode choices, which vary by variables. For example, the increase in the lowest temperature motivates middle-school students to choose active travel modes and cars. Humidity exceeding 50% is negatively correlated with the percentage of students walking. Increased PM2.5 concentration benefits the percentage of bike use but negatively affects public transport use. Moreover, O3 concentration has a V-shaped effect on walking and car use, which is the opposite of bike and public transport. These findings advance the understanding of effects of atmospheric conditions on middle-school students’ travel behavior and provide references for policymakers.