The measurement of the electron multiplying CCD(EMCCD) photoelectric performance parameters plays an important role in the development of the chip and imaging system. Measurement uncertainty is an important index to evaluate the quality of the measurement results. A measurement platform for EMCCD photoelectric performance parameters is set up. An EMCCD camera’s photoelectric performance parameters are measured based on photon transfer technique and the uncertainty of the measurement results is analyzed. Based on the method of GUM, the influences of the integrating sphere light source stability, EMCCD camera electronics system stability, installation posture, stray light in dark environment, camera's digital resolution and measurement sampling on the measurement results are analyzed. Based on the theoretical model of different photoelectric performance parameters, the uncertainty sources are discussed. The combined standard uncertainty is determined by the type A uncertainty and the type B uncertainty. The uncertainty evaluation model is established for the measurement of EMCCD photoelectric performance parameters, including convert gain, readout noise, full well, signal to noise ratio and multiplication gain. The uncertainty of the measurement results is calculated by using the established model. At last, we get the following results: relative standard uncertainty of the convert gain is 0.637% (k = 1), relative standard uncertainty of the readout noise is 0.653% (k = 1), relative standard uncertainty of the full well is 2.384% (k = 1), relative standard uncertainty of the signal to noise ratio is 2.301% (k = 1) and relative standard uncertainty of the multiplication gain is 1.259% (k = 1). The above uncertainty results show that the measurement results of this paper are accurate and reliable.