Functional constrained optimization (FCO) has emerged as a powerful tool for solving various machine learning problems. However, with the rapid increase in applications of neural networks in recent years, it has become apparent that both the objective and constraints often involve nonconvex functions, which poses significant challenges in obtaining high-quality solutions. In this work, we focus on a class of structured nonconvex FCO problems, where the two optimization variables are nonlinearly coupled in the inequality constraint. Leveraging the primal-dual optimization framework, we propose a smoothed first-order Lagrangian method (SLM) for solving this class of problems. We establish the theoretical convergence rates of SLM to the Karush-Kuhn-Tucker (KKT) solutions through quantifying dual error bounds. By establishing connections between this structured FCO and equilibrium-constrained nonconvex problems (also known as bilevel optimization), we apply the proposed SLM to tackle bilevel optimization problems where the lower-level problem is nonconvex. Numerical results obtained from both toy examples and hyper-data cleaning problems demonstrate the superiority of SLM compared to benchmark methods.