The aim of this study was to investigate the effects of organic carbon sources such as sugar, amino acids, and organic acids on the mycelial growth and spore production of root-rot pathogens of Panax notoginseng. Taking Fusarium solani and F. oxysporum as the research objects, the pure culture method was used to study the changes in mycelial growth and spore production of the root rot pathogen under the addition of 30 different organic carbon sources. Results indicate that after 6 days of cultivation, D-xylose, D-ribose, fructose, methionine, and oxalic acid had strong inhibitory effects on the growth of F. solani, with inhibition rates ranging from 20.3% to 32.3%. While D-xylose, D-ribose, fructose, trehalose, xylitol, and methionine had a strong suppressive activity against F. oxysporum, with inhibition rates ranging from 26.8% to 53.8%. There were significant differences in the effects of sugars and amino acids on spore production of the two pathogens. Among them, sugars can increase the spore production of F. oxysporum to varying degrees, while D-xylose, lactose and xylitol had a stronger inhibitory effect on F. solani, with inhibition rates ranging from 51.9% to 73.6%. All amino acids can significantly reduce the spore production of F. oxysporum, with the inhibition rates of methionine and phenylalanine being up to 80.7% to 89.1%, whereas proline, tryptophan, and phenylalanine can significantly increase the spore production of F. solani. The effects of organic acids on spore production of the two pathogens were similar. Malic acid, oxalic acid, and succinic acid can effectively reduce the spore production of the root rot pathogens, with inhibition rates ranging from 69.7% to 92.2%. In conclusion, organic carbon sources exert a significant impact on the mycelial growth and spore production of the root rot pathogens of P. notoginseng. Sugars were most effective at inhibiting mycelial growth, while amino acids had the strongest inhibitory effect on the spore production. Organic acids had the greatest variability in their effects on the spore production of the root-rot pathogen. The research results provide theoretical basis and data support for the development of green control strategies against P. notoginseng root-rot.