Light-emitting diodes (LEDs) are widely used in our daily lives. Both light and heat are generated from LED chips and then transmitted or conducted through multiple packaging materials and interfaces. Part of the transmitted light converts into heat along the light propagation; in return, the accumulation of heat leads to the degradation of light output. The accumulated heat negatively influences the reliability and longevity of LEDs, and thus thermal management is critical for LED packaging and applications. On the other hand, in LED packaging processes, many fluid flow problems exist, such as phosphor coating, silicone injection, chip bonding, solder reflow, etc. Amongst them, phosphor coating is the most important process which is essential for LED performance. Phosphor gel is a kind of non-Newton fluid and its coating process is a typical fluid-flow problem. Overall, since LED packaging and applications present many heat and fluid flow problems, obtaining a full understanding of these problems enables advancements in the development of LED processes and designs. In this review, the emphasis is placed on heat generation in chips, heat flow in packages and application products, fluid flow in phosphor coating process, etc. This is a domain in which significant progress has been achieved in the last decade, and reporting on these advances will facilitate state-of-the-art LED packaging and application technologies.