We study the linear-quadratic control problem for a class of non-exchangeable mean-field systems, which model large populations of heterogeneous interacting agents. We explicitly characterize the optimal control in terms of a new infinite-dimensional system of Riccati equations, for which we establish existence and uniqueness. To illustrate our results, we apply this framework to a systemic risk model involving heterogeneous banks, demonstrating the impact of agent heterogeneity on optimal risk mitigation strategies.