We demonstrate high-resolution and high-quality terahertz (THz) in-line digital holography based on the synthetic aperture method. The setup is built on a self-developed THz quantum cascade laser, and a lateral resolution better than 70 μm (～λ) is achieved at 4.3 THz. To correct intensity differences between sub-holograms before aperture stitching, a practical algorithm with global optimization is proposed. To address the twin-image problem for in-line holography, a sparsity-based phase retrieval algorithm is applied to perform the high-quality reconstruction. Furthermore, a new autofocusing criterion termed “reconstruction objective function” is introduced to obtain the best in-focus reconstruction distance, so the autofocusing procedure and the reconstruction are unified within the same framework. Both simulation and experiment prove its accuracy and robustness. Note that all the methods proposed here can be applied to other wavebands as well. We demonstrate the success of this THz synthetic aperture in-line holography on biological and semiconductor samples, showing its potential applications in bioimaging and materials analysis.