We propose a method named as double-scanning method, to improve the key rate of measurement-device-independent quantum key distribution (MDI-QKD) drastically. In the method, two parameters are scanned simultaneously to tightly estimate the counts of single-photon pairs and the phase-flip error rate jointly. Numerical results show that the method in this work can improve the key rate by $35%-280%$ in a typical experimental set-up. Besides, we study the optimization of MDI-QKD protocol with all parameters including the source parameters and failure probability parameters, over symmetric channel or asymmetric channel. Compared with the optimized results with only the source parameters, the all-parameter-optimization method could improve the key rate by about $10%$.
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