Key message The anatomical and physiological signaling pathways associated with successful scion-rootstock union in nurse seedling grafting of Camellia oleifera propagation are illustrated. Abstract Grafting, the successful union between scion and rootstock, has practical and biological importance. Nurse seedling grafting, as those practiced for Camellia oleifera, often results in high cell division activity and affinity, and is usually associated with significant rootstock and scion anatomical structures changes. However, a comprehensive explanation of signaling pathways, and how they affect graft union development, is still largely unknown. The present study investigates the union formation process in C. oleifera nurse seedling grafts and determines that it consists of six stages, namely, isolation layer formation, rootstock callus differentiation, scion callus differentiation, callus proliferation and connection, cambium differentiation and connection, and conducting tissue differentiation and connection, extending over a period of 35 days. Principal components analyses of the observed changes in physiology and protein expression identified three main factors contributing to the union formation process: cell proliferation, cell differentiation, and vascular bundle development. Further analysis showed that the regulation of the union formation process can be divided into two signaling pathways, namely, calcium and MAPK, which occur during vascular bundle development and cell proliferation and differentiation, respectively.