Flower-like MgO microparticles with excellent photocatalytic performance in degradation of various organic dyes (e.g., methylene blue, Congo red, thymol blue, bromothymol blue, eriochrome black T, and their mixture) were synthesized by a facile precipitation method via the reaction between Mg2+ and CO32− at 70 °C. The reaction time was found to be crucial in determining the final morphology of flower-like MgO. After studying the particles from time-dependent experiments, scanning electron microscope observation, Fourier transform infrared spectra and thermogravimetric analyses demonstrated that the formation of flower-like particles involved a complex process, in which agglomerates or rod-like particles with a formula of xMgCO3·yH2O (x = 0.75–0.77 and y = 1.87–1.96) were favorably formed after the initial mixture of the reactants. Owing to the chemical instability, they would turn into flower-like particles, which had a composition of xMgCO3·yMg(OH)2·zH2O (x = 0.84–0.86, y = 0.13–0.23, and z = 0.77–1.15). After calcination, the generated product not only possessed a superior photocatalytic performance in degradation of organic dyes (100 mg L−1) under UV light irradiation in contrast to other morphologies of MgO and other related state-of-the-art photocatalysts (e.g., N-doped TiO2, Degussa P25 TiO2, ZnO, WO3, α-Fe2O3, BiVO4, and g-C3N4), but also could be used for five cycles, maintaining its efficiency above 92.2%. These capacities made the flower-like MgO a potential candidate for polluted water treatment. Also, the underlying photocatalysis mechanism of MgO was proposed through radical trapping experiments.