Ammonium ions have positive effects on the sulfidization flotation of malachite; however, the underlying mechanisms remain poorly understood. In the present work, micro-flotation tests, field emission scanning electron microscopy (FESEM), energy dispersive spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and solution analysis for ammonium nitrogen were carried out. The flotation results showed positive effects of ammonium on the sulfidization flotation of malachite. Macroscopically, the sulfidized malachite produced with ammonium exhibited a darker color than that without ammonium, whereas the opposite appeared to be true for their corresponding residual liquids. FESEM images highlighted the larger particle size and higher converge density of the sulfidization product when the presence of ammonium. Furthermore, XPS results indicated a higher sulfur concentration on malachite surfaces when the presence of ammonium. XRD results showed that Cu31S16 (djurleite) and Cu7S4 (anilite) comprised the sulfidization products, regardless of the presence or absence of ammonium. However, neither EDS nor XPS analysis showed nitrogen on malachite surfaces; moreover, the residual-ratio results for ammonium nitrogen clearly demonstrated that most ammonium continued to be held in solution before and after malachite sulfidization. Based on these findings, we inferred that ammonium ions may mediate the nucleation and growth of sulfidization product during malachite sulfidization, rendering larger sulfidization product particles. The larger size of sulfidization products may result in a darker, stabler and denser sulfidization product coating layer, and then may reduce the generation of colloidal copper sulfide in the residual liquids. Ultimately, ammonium facilitates better performance of sulfidization flotation of malachite.