Conventional optical microscopy provides only intensity images, for which the contrast is induced by fluorescence or the absorption of the sample on the illumination light. Yet, the phase, polarization, and spectrum information of the sample is lost. Meanwhile, limited by design, conventional optical microscopy suffers from the conflict between spatial resolution and field of view (FOV). Modulated illuminations based computational microscopy (CM), which joints front-end optics and post-detection signal processing can, in general, extend the capability of conventional microscopy; for example, it allows the acquisition of the intensity, phase, polarization information, and enhance the spatial resolution within a large FOV. In this paper, modulated illumination based CM was exploited for implementation of phase imaging, resolution enhancement, dual-modality imaging. First, modulated illumination based CM provides quantitative amplitude and phase images, revealing the 3D shape and the inner structure of transparent or translucent samples in the absence of fluorescent labeling. Second, pupil-segmentation based CM measures the aberration of focus modulation microscopy (FMM). Hence, the resolution and SNR of FMM was enhanced after the aberration compensation. Third, phase and fluorescence dualmodality imaging was implemented in confocal laser scanning microscopy (CLSM) by extending the depth of field (DOF) of the CLSM system with a tunable acoustic gradient index of refraction (TAG) lens, providing complementary information (structural/functional) with pixel-to-pixel correspondence for the same sample. Furthermore, the combination of the two imaging modalities enables standalone determination of the refractive index of live cells. © 2020 SPIE.