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Aiming at the problem that the traditional digital holographic microscopic reconstruction method is difficult to obtain the best reconstruction distance and it is difficult to be portable on the traditional PC platform, an embedded autofocus system for digital holographic microscopy is designed. The system can not only realize the autofocus of digital holographic microscopic imaging, but also achieve the best reconstruction effect, and has the characteristics of portability. The system adopts coaxial optical path configuration with image sensor to acquire holograms, and uses the optimized angular spectrum algorithm to perform holographic reconstruction. Combined with the second generation wavelet algorithm to evaluate the reconstruction results, the proposed system finds the best reconstruction distance according to the evaluation results, and obtain the best reconstruction results at the same time. The system is used to collect a batch of resolution plate holograms for autofocus test to verify the feasibility of the proposed method. Experiments show that the reconstruction speed of the system is 0.6s, the resolution is 3.48um, and the autofocus accuracy rate is over 90%. The experimental results verify the effectiveness of the system.