Many proteins could aggregate into amyloid fibrils under certain conditions. However, the aggregation process and morphology of the fibrils may be significantly different because of the distinct protein structure. In this article, the hydrophilic carbon dots (Lys‐CA‐CDs) were prepared using lysine (Lys) and citric acid (CA) as reactant under the assistance of a microwave. The dissimilar modulation effect of Lys‐CA‐CDs on the aggregation process of distinct structure protein was further investigated, where bovine serum albumin (BSA) and hen egg white lysozyme (HEWL) were chosen as model proteins. All results showed that Lys‐CA‐CDs displayed the contrary influence on the aggregation process of BSA and HEWL. Lys‐CA‐CDs could induce BSA to aggregate into more wormlike fibrils and inhibit the aggregation of HEWL into hair‐like fibrils. The influence on the aggregation process of BSA may be assigned to the increased concentration of BSA around the Lys‐CA‐CDs caused by their interaction. However, inserting of Lys‐CA‐CDs into the inner structure of HEWL led to the change of protein secondary structure. The change of secondary structure further made it difficult for HEWL to aggregate into fibrils and Lys‐CA‐CDs showed the inhibition effect on HEWL aggregation.