e23549 Background: Cardiac myxoma is a commonly encountered tumor within the heart that has the potential to be life-threatening. However, the cellular composition and molecular characteristics of this condition are still not well understood. Methods: We performed single-cell sequencing on cardiac myxoma tissues obtained from 5 patients, focusing on the identification and characterization of cellular subtypes, cell trajectory analysis, and intercellular communication analysis. We performed a comparative analysis of the changes in cell types and states between cardiac myxoma and normal heart tissues. Furthermore, we retrospectively collected pathological sections from 49 cardiac myxoma cases and employed the multi-color immunohistochemistry (mIHC) technology to analyze the relationship between cellular infiltration and the severity of disease. Results: In total, 75,641 cells in cardiac myxoma tissues formed 9 distinct cell populations. Myxoma cells exhibited a significant resemblance to fibroblasts, yet they were distinguished by an increased expression of phosphodiesterases and genes associated with cell proliferation, differentiation, adhesion, and migration. Myxoma cells displayed cellular heterogeneity and demonstrated two distinct evolutionary pathways. One involves the transition from stem cell-like cells to stromal cells and the other involves enhancement of blood coagulation function. Immune cells surrounding the myxoma displayed suppressive features, with the presence of CD8+ T cells expressing TOX and GZMK, as well as a decrease in the secretion of cytotoxic molecules, indicating an impaired effector function. Macrophages were found to express growth factors such as EREG and PDGFC which played a role in promoting myxoma growth. Conversely, myxoma cells were also observed to secrete ANGPTL4 and ANXA1 which in turn induced the transformation of CD206+ macrophages. Extensive mIHC experiments indicated that a higher proportion of CD206+macrophages and myxoma cells infiltrating the myxoma tissues, along with their enhanced spatial interaction, were found to significantly contribute to the increased occurrence of embolism in cardiac myxoma patients. Conclusions: In summary, this study presents a comprehensive single-cell atlas of cardiac myxoma, highlighting the heterogeneity of myxoma cells and their collaborative impact on immune cells. These findings shed light on the complex pathobiology of cardiac myxoma and present potential targets for intervention.