The quality of wire bonding is an important factor in the manufacturing of various precision electronic components in semiconductor industry. The wire bonding defects, including high loop and low loop, determined by the bonding height information, inevitably affect the performance of the product. It is vital to measure height information quickly and accurately to reduce the failure rate in the manufacturing process. However, traditional measurement system often needs to move the target samples for a number of times. To address the key measurement problems, a three-dimensional (3D) optical measurement system is developed based on autostereoscopy technologies. A micro-lens array is used to divide the light emitted by the sample into different directions. The elemental images from different view angles contain original 3D information and is recorded by a high-resolution image sensor. On the basis of the multi-view stereo information contained in the image, the elemental images can be refocused into multi-focus images. The 3D information can be directly extracted from the multi-focus images through self-developed algorithms. Experiment results show that the system can complete the measurement in 2 seconds and reach a high measurement accuracy at a sub-micrometer level. This verifies the feasibility of the proposed measurement system which is efficient and accurate for 3D inspection of wire bonding.