Cities are growing higher and denser, and understanding and constructing the compact city form is of great importance to optimize sustainable urbanization. The two-dimensional (2D) urban compact form has been widely studied by previous researchers, while the driving mechanism of three-dimensional (3D) compact morphology, which reflects the reality of the urban environment has seldom been developed. In this study, land surface temperature (LST) was retrieved by using the mono-window algorithm method based on Landsat 8 images of Xiamen in South China, which were acquired respectively on 14 April, 15 August, 2 October, and 21 December in 2017, and 11 March in 2018. We then aimed to explore the driving mechanism of the 3D compact form on the urban heat environment (UHE) based on our developed 3D Compactness Index (VCI) and remote sensing, as well as Geo-Detector techniques. The results show that the 3D compact form can positively effect UHE better than individual urban form construction elements, as can the combination of the 2D compact form with building height. Individually, building density had a greater effect on UHE than that of building height. At the same time, an integration of building density and height showed an enhanced inter-effect on UHE. Moreover, we explore the temporal and spatial UHE heterogeneity with regards to 3D compact form across different seasons. We also investigate the UHE impacts discrepancy caused by different 3D compactness categories. This shows that increasing the 3D compactness of an urban community from 0.016 to 0.323 would increase the heat accumulation, which was, in terms of satellite derived LST, by 1.35 °C, suggesting that higher compact forms strengthen UHE. This study highlights the challenge of the urban 3D compact form in respect of its UHE impact. The related evaluation in this study would help shed light on urban form optimization.