In order to capture accurate data of laser-driven fusion test, diagnostic instruments(DI) which are mounted onto diagnostic instrument manipulator(DIM) should align the target with tight tolerance. Traditional alignment methods have problems of time consumption and error large. An accurate automatic alignment method was introduced, which based on visual servoing according to the virtue of DIM and DI. First, a 3D alignment vector was constructed to estimate the target deviation in the stereo vision system. Under narrow field of view, estimated value was close to true deviation. Second, a 3 DOF pose adjusting mode was founded to promote motion accuracy. Finally, a visual servo controller based on the alignment vector and pose adjustment mode was designed. The process of alignment needs offline calibration only once. Through the three steps, DI can automatic align the target with high accuracy. Test indicates that alignment accuracy(RMS) is 11 μm in x direction and 12 μm in y direction. Laser shot test with X-ray framing camera show that the automatic align method can satisfy the project requirements.