Lymphatic endothelial cells (LECs) have long been viewed as passive conduits that merely maintain tissue fluid homeostasis. But that picture has changed dramatically. Recent advances in single-cell transcriptome sequencing (scRNA-seq) and spatial transcriptomics (ST) have revealed that LECs are highly heterogeneous and remarkably plastic in their functions. This review summarizes the new research results of LECs based on the above two technologies. LECs in normal tissues have multiple types of subpopulations. In the lymph node, there are further sub-regions, such as the subcapsular sinus ceiling/floor LECs, medullary sinus LECs, valve LECs and other special subsets. Each subpopulation performs distinct functions depending on its anatomical location, ranging from lymph drainage and barrier formation to immune regulation, etc. Under pathological conditions such as cancer, chronic inflammation, cardiovascular disease, obesity, and tissue repair, LECs undergo profound transcriptional reprogramming and phenotypic remodeling. They express immune checkpoint molecules, secrete chemokines, and build ligand-receptor interaction networks. In other words, LECs transform from passive structural pipes into active signaling integration centers and immune regulatory hubs. They participate directly in immune response modulation, metastasis promotion or suppression, tissue repair, and fibrosis. These findings have fundamentally redefined the biological role of LECs in the microenvironment. Targeting LECs heterogeneity and their bidirectional cell-cell interaction networks may offer novel stromal-targeted strategies for intervening in tumor lymphatic metastasis, reversing chronic inflammation, and treating cardiovascular diseases.