As the fundamental dispositional determinant of social motivation, social value orientation (SVO) may modulate individuals' response patterns in interpersonal coordination contexts. Adopting fNIRS-based hyperscanning approach, the present investigation uncovered the hyper-brain network topological dynamics underlying the effect of the dyadic similarity in the social value orientation on interpersonal coordination. Our findings indicated that the dyads in proself group exhibited the higher degree of competitive intensity during the competitive coordination block, and the dyads in the prosocial group exhibited a higher degree of cooperative coordination during the cooperative coordination block. Distinct hyper-brain functional connectivity patterns and network topological characteristics were identified during the competitive and cooperative coordination blocks in the proself and prosocial groups. The nodal-network global efficiency at the right frontopolar area further mediated the effect of the dyadic deviation in social value orientation similarity on effective adjustments after the negative feedback during the cooperative coordination block in the prosocial group. Our findings manifested distinct behavioral performances and hyper-brain functional connectivity patterns underlying the effect of the dyadic similarity in social value orientation on interpersonal coordination in the real-time mode.