To date, much attention has been paid to phytochemicals because of their diverse pharmacological effects on a variety of diseases such as cancer. In this regard, computer-aided drug design, as a cost- and time-effective approach, is primarily applied to investigate the drug candidates before their further costly in vitro and in vivo experimental evaluations. Accordingly, different signaling pathways and proteins can be targeted using such strategies. As a key protein for the initiation of eukaryotic DNA replication, mini-chromosome maintenance complex component 7 (MCM7) overexpression is related to the initiation and progression of aggressive malignancies. The current study was conducted to identify new potential natural compounds from the yellow sweet clover, Melilotus officinalis (Linn.) Pall, by examining the potential of 40 isolated phytochemicals against MCM7 protein. A structure-based pharmacophore model to the protein active site cavity was generated and followed by virtual screening and molecular docking. Overall, four compounds were selected for further evaluation based on their binding affinities. Our analyses revealed that two novel compounds, namely rosmarinic acid (PubChem CID:5281792) and melilotigenin (PubChem CID:14059499) might be druggable and offer safe usage in human. The stability of these two protein-ligand complex structures was confirmed through molecular dynamics simulation. The findings of this study reveal the potential of these two phytochemicals to serve as anticancer agents, while further pharmacological experiments are required to confirm their effectiveness against human cancers.