Land-surface heterogeneity comes in many varieties and occurs over a wide range of spatial scales. In urban environments, micro-scale momentum heterogeneity resulting from urban canopy, convective scale thermal heterogeneity resulting from anthropogenic heat and unequal heating rates between urban and rural surfaces, as well as large-scale mean pressure gradient simultaneously influence the flows and transport of scalars. However, the mechanisms by which multi-scale surface heterogeneity impacts flows and scalar transport across different spatial scales remain uncertain. The overarching goal of this work is to understand how the multi-scale surface heterogeneity of cities influences flows, temperature, humidity, the transport of heavy particles, and cloud formation in urban environments. The primary research method used is numerical simulation through large-eddy simulations (LES). Additionally, Reynolds-averaged Navier-Stokes (RANS) simulations, observational data, and analytical approaches are also employed. CHAPTER 1 presents a general review of the challenges in understanding flows and transport of scalars over land surface of multi-scale surface heterogeneity. CHAPTER 2 investigates the impact of surface heterogeneity and time-varying surface temperatures on local meteorological quantities such as air temperature and humidity. The results show that time-varying surface temperature over different surface types leads to distinct temporal change in flows and meteorological quantities. The overall thermal comfort in urban areas close to open water surface can be compromised by higher humidity closer to the lake shore. CHAPTER 3 explores how urban canopy affect the transport of heavy particles. The results show that urban canopy greatly reduces the horizontal mean wind within the canopy sub-layer, therefore affecting the dispersion of heavy particles both within and above the canopy sub-layer. Urban canopy reduces the vertical transport of heavy particles emitted from ground surface to the region above urban canopy. CHAPTER 4 investigates the influence of momentum and thermal surface heterogeneities at different spatial scales on wind and temperature in coastal urban environments. An analytical model is proposed to explain the finding that urban canopy enhances canopy layer urban heat island (UHI) intensity. The effect of urban canopy is considered in terms of an additional vertical velocity scale that facilitates heat transport from the heated surface and therefore increases UHI intensity. This work highlights the importance of the momentum roughness elements to the transport of heat. CHAPTER 5 analyzes how momentum and thermal surface heterogeneities in micro-scale and convective scale modify flows and boundary-layer cloud formation in urban environments. LES results show that different urban morphological types across different cities could modify cloud cover at local scale, which can be supported by the observational evidence. Conclusion and future work are presented in CHAPTER 6.