Adaptive optics (AO) has been instrumental in ophthalmic imaging, by correcting wavefront aberrations in ocular optics and achieving diffraction-limited resolution. Current state-of-the-art AO retinal imaging systems use mirror-based optics to avoid surface reflection and chromatic aberrations, requiring a large system footprint with long focal length spherical mirrors. Here we report a compact refractive lens-based AO scanning laser ophthalmoscopy (SLO) system with simultaneous dual channel fluorescence imaging capacity in mouse retina. The optical layout fits on a 2 x 2 inch optical breadboard and the whole system is constructed on a mobile 3x4 inch optical table. We show that the 3D image resolutions achieved are significantly improved with AO correction, particularly in the z-axis (2x improvement compared to without AO, approaching diffraction-limited resolution). The optical design enables survey of a relatively large retinal area, up to 20 degree field of view, as well as higher magnification AO imaging. Interestingly, resolution and signal improvements with AO are still observed over a larger field of view. Simultaneous imaging with 488nm and 561nm laser lines was evaluated using dual channel AOSLO in CX3CR1-GFP transgenic mice expressing EGFP in microglia, undergoing rhodamine angiography. We performed dynamic high-resolution 3D imaging of microglial morphology every 5 mins for one hour and longitudinally over 3 weeks, demonstrating microglial activation and translocation over short and long time periods in an optic nerve crush model. This lens-based compact AOSLO offers a versatile and compact design for retinal fluorescence imaging in mice.