In this study, a novel adaptive wavefront correction (AWC) technique is implemented on a compactly developed structured illumination holographic tomography (SI-HT) system. We propose a mechanical movement-free compact scanning architecture for SI-HT systems with AWC, implemented by designing and displaying a series of computer-generated holograms (CGH) composed of blazed grating with phase Fresnel lens on a phase-only spatial light modulator (SLM). In the proposed SI-HT, the aberrations of the optical system are sensed by digital holography and are used to design the CGH-based AWC to compensate the phase aberrations of the tomographic imaging system. The proposed method was validated using a standard Siemens star target, its potential application was demonstrated using a live candida rugosa sample, and its label-free three-dimensional refractive index profile was generated at its subcellular level. The experimental results obtained reveal the ability of the proposed method to enhance the imaging performance in both lateral and axial directions.