We present an improved statistical fluctuation analysis for measurement-device-independent quantum key distribution with a three-intensity decoy-state method. Taking the statistical fluctuations for different sources jointly, we present more tightened formulas for some key quantities used in calculating the secure final key. Numerical simulation shows that, given the total number of pulses
1012, our method improves the key rate by about 97% for a distance of 50 km compared with the result given by Xu et al. [F. Xu et al., Phys. Rev. A 89, 052333 (2014)], and improves the key rate by
145 for a distance of 100 km compared with the result from full optimization of all parameters but treating the statistical fluctuations traditionally, i.e., treating the fluctuations for different sources separately.