A novel upgraded molecular mechanics framework has been developed by improving the flexural and torsional behavior in bonds between atoms based on modified couple stress theory (MCS-MM). The MCS-MM approach drives a considerable advancement in predicting the mechanical behavior of nanostructures. Due to applying the modified couple stress theory in the beam energy equations, the length scale parameter is added to the equations. The presented method provides a better prediction for the elastic and geometric properties of the equivalent beams in the atomic structure. In order to show the efficiency of this upgraded proposed model, various aspects of graphene sheets were considered, such as energy deviation, mechanical properties, buckling behavior, and crack opening displacement (COD). The results confirm the efficiency and accuracy of the model and are consistent with molecular dynamics modeling. The MCS MM method leads to a significant improvement in strain energy deviation. It predicts the elastic properties and mechanical behavior of graphene sheets more accurately. The MCS-MM method can be replaced with previous ones as an appropriate approach.