IEEE 802.11be (Wi-Fi 7) introduces a new concept called multi-link operation (MLO) which allows multiple Wi-Fi interfaces in different bands (2.4,5, and 6 GHz) to work together to increase network throughput, reduce latency, and improve spectrum reuse efficiency in dense overlapping networks. To make the most of MLO, a new intelligent resource allocation is needed. This paper proposes a model to align MLO and access point (AP) coordination in 11be. To maximize network throughput, a network topology optimization problem is formulated for MLO with AP coordination, which is solved by exploiting the totally unimodular property of the bipartite graph formed by the connection between AP and station (STA) in Wi-Fi networks. Subsequently, a proportional fairness algorithm is applied for radio link allocation, network throughput optimization considering the channel condition, and the fairness of the multi-link device (MLD) data rate. The performance of the proposed algorithm on two main MLO implementations -multi-mink multi-radio (MLMR) with simultaneous transmission and reception (STR), and the interplay between multiple nodes employing them are evaluated through cross-layer (PHY-MAC) data rate simulation with PHY abstraction.