Precipitates are critical in strengthening Mg-Gd-Y-Zn-Mn alloys. However, lack of sufficient atomic-scale characterization restricts further understanding of the precipitates. Therefore, in the present study, precipitates in the as-cast, solution-annealed, and isothermally aged (200 °C) Mg-Gd-Y-Zn-Mn alloy have been comprehensively examined on the atomic scale by aberration-corrected (Cs) high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM) combined with energy dispersive X-ray spectrometry (EDS). When observed in the [0001]α direction in the early-aged alloy for 6 min, uneven local rare earth solute clusters in the form of βH and βZ phases suggest a transition from βH to βZ. In the peak-aged alloy for 16 h, Mn atoms are found to segregate into the γ′/long-period stacking ordered (LPSO) phase and β′ phase, participating in their formation. In the over-aged alloys for 200 h, γ″ phase is detected with enrichment of Mn, coexisting with the γ′ and β′ phases. Furthermore, β″-like structures are observed, which may be defective βM or β′T as a result of their overlapping, thus providing a possible explanation for the controversy regarding the existence of the β″ phase. Our findings serve as evidence that deepens the understanding of the precipitates in Mg-Gd-Y-Zn-Mn alloys at the atomic level.