Physarum polycephalum inspired algorithm (PPA), also known as the Physarum Solver, has attracted great attention. By modelling real-world problems into a graph with network flow and adopting proper equations to calculate the distance between the nodes in the graph, PPA could be used to solve system optimization problems or user equilibrium problems. However, some problems such as the maximum flow (MF) problem, minimum-cost-maximum-flow (MCMF) problem, and link-capacitated traffic assignment problem (CTAP), require the flow flowing through links to follow capacity constraints. Motivated by the lack of related PPA-based research, a novel framework, the capacitated physarum polycephalum inspired algorithm (CPPA), is proposed to allow capacity constraints toward link flow in the PPA. To prove the validity of the CPPA, we developed three applications of the CPPA, i.e., the CPPA for the MF problem (CPPA-MF), the CPPA for the MCFC problem, and the CPPA for the link-capacitated traffic assignment problem (CPPA-CTAP). In the experiments, all the applications of the CPPA solve the problems successfully. Some of them demonstrate efficiency compared to the baseline algorithms. The experimental results prove the validation of using the CPPA framework to control link flow in the PPA is valid. The CPPA is also very robust and easy to implement since it could be successfully applied in three different scenarios. The proposed method shows that: having the ability to control the maximum among flow flowing through links in the PPA, the CPPA could tackle more complex real-world problems in the future.