Reference material is of great significance to the measurement accuracy of X-ray energy/wave dispersive spectrometer (EDS/WDS). In this work a reference material of manganese (Mn) content (mass fraction, %) of pure Mn flake for EDS/WDS calibration was developed. The surfaces of Mn flakes were finely treated by mechanical grinding and argon ion polishing, and the Mn flakes with high cleanliness and low roughness were obtained. The homogeneity and stability of Mn content of the Mn flakes were analyzed carefully using electron probe micro-analyzer (EPMA). The Mn content of the reference material was determined using inductively coupled plasma optical emission spectrometer (ICP-OES) and inductively coupled plasma mass spectrometry (ICP-MS). The sources of uncertainty components of Mn reference material were fully analyzed and evaluated. The results show that the homogeneity of the pure Mn flake reference material meet the requirements. The Mn content of the vacuum-packed pure Mn flake is stable for up to one year at ambient temperature. The Mn content reference material of the pure Mn flake reference material is 99.5 %, and its expanded uncertainty is 0.9 % (k = 2). The pure Mn flake reference material can meet the calibration requirements of X-ray EDS/WDS, and guarantee the accuracy and consistency of measurement results. The content of this study complies with the definition of reference materials in ISO 17034 and can be used to calibrate measurement systems. The Mn content reference material can be widely used for element measurement in the fields of scientific research, manufacturing and trade activities.