Over the past few years, non-destructive testing plays an increasingly important role in the accuracy detection of PCB manufacturing. Due to the complexity of PCB materials and the development of PCB towards high density. So far, no method has been described which can semi-automatically detect the machining accuracy of PCB array holes based on three-dimensional structural data. Here, we propose an efficient method to detect the machining accuracy of PCB array holes by X-ray micro-CT. Firstly, the overall three-dimensional structural data of the sample was obtained by CT scanning and three-dimensional reconstruction. And then all the information of array holes could be extracted and visual analyzed. Finally, the measured values of PCB machining accuracy were gained according to the designed algorithms, such as straightness error, process capability index, cylindricity error and three-dimensional surface roughness. The method that based on X-ray micro-CT can get the results of PCB array holes' machining accuracy precisely and efficiently. The same principle also provides a direction for promoting the development of micro-CT in PCB industry.