Reconfigurable intelligent surfaces (RISs) have the potential to significantly enhance the performance of integrated sensing and communication (ISAC) systems, particularly in line-of-sight (LoS) blockage scenarios. However, as larger RISs are integrated into ISAC systems, mutual coupling (MC) effects between RIS elements become more pronounced, leading to a substantial degradation in performance, especially for localization applications. In this paper, we first conduct a misspecified and standard Cram\'er-Rao bound analysis to quantify the impact of MC on localization performance, demonstrating severe degradations in accuracy, especially when MC is ignored. Building on this, we propose a novel joint user equipment localization and RIS MC parameter estimation (JLMC) method in near-field wireless systems. Our two-stage MC-aware approach outperforms classical methods that neglect MC, significantly improving localization accuracy and overall system performance. Simulation results validate the effectiveness and advantages of the proposed method in realistic scenarios.