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In the present paper, we successfully prepared PbS microcrystals with a flower-shaped structure in a simple aqueous system using microwave irradiation and systematically researched various factors affecting the growth of the flower-shaped PbS crystals. Experimental results indicated that the change of the molar ratio of Pb2+/S2O3 2- could significantly influence the morphology of the product while keeping the other experimental conditions constant: with the decrease of the molar ratio of Pb2+/S2O3 2- from 1:1 to 1:4, the shapes of the products varied from rod to cuboid to flower. Changing the irradiation power in a small range (10−40%) had little effect on the shape of the product. When thiourea and thioacetamide were used as sulfur ion sources instead of Na2S2O3, the shapes of the as-obtained PbS crystals were dendritic and platelike, respectively. The above results further confirmed that Na2S2O3 played an important role in the formation process of PbS crystals with the flower-shaped structure. At the same time, transmission electron spectroscopy observations showed that the counterions for Pb2+ could influence the shape of the product: when Pb(NO3)2 and PbCl2 were used as the lead ion sources, cuboid PbS crystals were produced; while when PbSO4 was used as the lead ion source, the flower-shaped PbS crystals were obtained. A growth mechanism of the flower-shaped PbS crystals was proposed.