Buildings, as a crucial element of the cities, plays an important role in altering surface energy partitioning and regulating microclimate. Quantifying the relationship between architectural three-dimensional morphology and atmosphere-soil energy processes/microclimate is of great importance to climate resilient city. This paper investigates the relationships between architectural three-dimensional fractal/three-dimensional shape index and atmosphere-soil energy processes/air temperature/air relative humidity based on multiple scenario simulations using ENVI-met by adopting a method of boosted regression trees (BRTs). The results show that in daytime, non-linear relationships exist between three-dimensional fractal/three-dimensional shape index and atmosphere-soil energy processes (the net radiation, soil heat flux, storage of heat in buildings, sensible flux, and latent flux)/air temperature/air relative humidity. In daytime, when the three-dimensional fractal increases from 2.4 to 2.6 or the three-dimensional shape index increases from 1.0 to 2.0, these two indicators exhibit a stepwise negative correlation with the net radiation, soil heat flux, storage of heat in buildings, sensible flux, latent flux, and air temperature, respectively. The 3D fractal shows a positive correlation with air relative humidity. With 3D shape index increases, the air relative humidity changes slightly. At night, when the 3D fractal changes higher than 2.4, the 3D fractal shows a negative correlation with sensible flux and air temperature, while a positive correlation with soil heat flux and latent flux. At night, when the 3D shape index changes lower than 2.0, the 3D shape index exhibits a negative correlation with air temperature and relative humidity. In daytime, when the 3D shape index ranges from 2.0 to 2.5, the 3D shape index shows a negative correlation with sensible flux and latent flux; And when the 3D shape index exceeds 2.5, there is no statistically correlation between the 3D shape index and energy indicators. In daytime, the impact amplitudes of the three-dimensional fractal on atmosphere-soil energy processes (the net radiation, soil heat flux, storage of heat in buildings, sensible flux, and latent flux)/air temperature/air relative humidity are 1.0 W/m², 7.0 W/m², 15.0 W/m², 20.0 W/m², 10.0 W/m², 0.2℃, respectively. The impact amplitudes of the three-dimensional shape index on atmosphere-soil energy processes/air temperature/air relative humidity are 0.5 W/m², 3.0 W/m², 10.0 W/m², 10.0 W/m², 10.0 W/m², 0.05℃, respectively. These findings can provide quantitative insights for regulating atmosphere-soil energy processes and microclimate via design of 3D architectural morphology. Given the direct insights provided, the BRTs method is recommended for exploring the relationships between architectural morphology and atmosphere-soil energy processes/micrometeorology.