In conventional electrical discharge machining (EDM), the workpiece material is considered as homogenous material. When a micro feature is machined in alloy by micro EDM, microstructure of alloy may be of the same order as the micro feature. This may lead to the variation of machining performance of micro EDM. This paper demonstrates the influence of material microstructure on the machining performance by drilling micro holes within the crystal grain and on the boundary of TA0-1. Experimental results indicate that the average values of material removal rate, tool wear ratios and the discharge gaps on different locations are different because their material properties are different.