In silicon single crystal micro-electrical discharge machining (Micro-EDM), the plasma channel and workpiece temperature field directly affect the machined parts. For Si single crystal, with short single discharge time and small inter-electrode gap, the temperature cannot be easily measured directly. Based on the theory of energy conservation and heat conduction, combined with Micro-EDM process, in this paper, thermodynamic analysis of plasma in Micro-EDM process is conducted, and a plasma temperature distribution model considering latent heat of fusion is established. Adopting Gaussian distribution heat flux boundary condition and the temperature field distribution of the workpiece surface is simulated by FLUENT. The relationship between material removal rate (MRR) and surface roughness (SR) corresponding to temperature distribution under different peak current and pulse width conditions is analyzed. The results show that plasma temperature has a positive correlation with peak current and pulse width. The increase of peak current and pulse width within the processing parameter range leads to the increase of MRR and SR. The experimental results verify the correctness of the model.