Rose black Leaf lesion is one of the most severe diseases affecting roses and impacts the growth and ornamental value of rose plants. In this study, Marssonina rosae and Alternaria alternata were frequently isolated simultaneously from rose leaves exhibiting black Leaf lesion disease symptoms, and their pathogenicity was confirmed by Koch's postulates. In dual culture assays, M. rosae and A. alternata were co-cultured for their preliminary characterization, and the liquid culture filtrate of M. rosae promoted the growth of A. alternata. The interactions between M. rosae and A. alternata were investigated through in vitro leaf inoculation with M. rosae inoculated first, followed by A. alternata sequentially at 0, 4, or 6 days later, while the controls were inoculated with M. rosae or A. alternata individually. The results showed that the lesion area of the rose black Leaf lesion and the spore concentration of M. rosae on leaf surfaces significantly increased if M. rosae was inoculated four days prior to A. alternata subsequent inoculation. Moreover, comparative expression analyses were performed of several genes involved in plants' reactions to pathogens, such as the master regulators of salicylic acid (SA) or jasmonic acid (JA)-mediated defense signaling pathway networks. The results indicated that in susceptible roses, the inhibition of SA-related defense signaling through increasing SA levels in the early stage of M. rosae infection (0-4dpi) led to continued inhibition of a large number of plant–pathogen interaction-related and signaling-related genes, including OPR3, ICS, NPR1, MYC2, and WRKY70, which facilitated the invasion of Alternata as a saprophytic fungus. In the later stages of the disease (8–10 dpi), The expression of SA-related resistance genes was gradually decreased, and the antagonistic effect of SA on the JA pathway was weakened, which increased the pathogenicity and sporulation capacity of M. rosae and reduced the pathogenicity of A. alternata. In conclusion, this study demonstrated that the co-infection by two fungi exacerbated the severity of rose black Leaf lesion disease through the regulation of SA- and JA-mediated resistance signaling pathways to promote the invasion of A. alternaria and further enhance the pathogenicity of M. rosae. The findings of this study revealed a new mechanism underlying the occurrence of rose black Leaf lesion disease, providing a novel theoretical framework and guidance for the prevention and control of this disease in roses.