Direct-seeding rice has grown in popularity in recent years and is widespread in China. This study focused on the effects of pig slurry (PS) on grain quality and safety in direct-seeding rice. Application of more than 210 m3·hm−2 increased rice yield and dry matter accumulation, compared with conventional chemical fertilizer treatment (CK2). At the heading and maturing stage, a high dosage of PS (T6, T8 and T9 treatments) promoted uptake of Pb, Cu, Zn, Fe and Mn by rice plants and grain, but retarded uptake of Cr, Co and Ni, indicating an ability to alleviate toxicity of some heavy metals. Compared with CK2, PS alleviated the transfer of Pb, Cr, Co, Ni and Cu from straw to grain, but enhanced the transport of Zn, Fe and Mn. Although PS application slightly diminished the processing quality, including brown rice, milled rice and head milled rice, it significantly decreased the amylose content, optimized the starch profile, and improved the overall quality. The results confirmed the feasibility and safety of PS application to direct-seeding rice, and determined that PS basal and panicle fertilizer could increase yield and improve the rice quality when applied between 210 and 240 m3·hm−2.