Introduction: Tobacco brown spot, caused by Alternaria spp., reduces tobacco yield and quality. Monitoring airborne spores is essential for early warning, but the vertical distribution of Alternaria spores within tobacco canopies and its relationship with meteorological factors remain poorly understood. This study aimed to determine the optimal sampling height for Alternaria spores in tobacco fields and to analyze height-dependent correlations with environmental variables. Methods: Field experiments were conducted in Fuquan City, Guizhou Province, China, in 2025 using susceptible (Yunyan 87) and moderately resistant (Guiyan 20) tobacco cultivars. Airborne spores were collected using the slide method at three heights (0.5, 1.0, and 1.5 m) and two locations (field center and edge). Meteorological variables, including air temperature, relative humidity, soil temperature, wind speed, total rainfall, and light intensity, were recorded. Relative proportions of spores at each height were calculated, and Pearson and lagged correlation analyses were performed. Results: Spore counts were significantly higher in Yunyan 87 than in Guiyan 20, and higher at the field center than at the edge for both cultivars. The 1.0 m height captured the highest relative proportion of spores (51.8%), followed by 1.5 m (25.3%) and 0.5 m (22.9%). Spore abundance was negatively correlated with air temperature, wind speed, and light intensity, and positively correlated with relative humidity and rainfall. Rainfall showed the strongest positive correlation at a 2-day lag (r = 0.49–0.52). Spores collected at 1.5 m exhibited stronger correlations with wind speed, rainfall, and light intensity than those at lower heights. Discussion: The middle canopy height (1.0 m) is recommended for spore trap placement at the field center. The height-dependent correlations suggest that meteorological factors exert greater influence on spore dispersal to higher altitudes than on local sporulation. These findings improve understanding of spore spatial distribution and provide a foundation for predictive models of tobacco brown spot. Limitations include the 17-day single-season sampling and the passive slide method; future studies with longer periods and active traps are needed.