Modality-agnostic Semantic Segmentation (MaSS) aims to achieve robust scene understanding across arbitrary combinations of input modality. Existing methods typically rely on explicit feature alignment to achieve modal homogenization, which dilutes the distinctive strengths of each modality and destroys their inherent complementarity. To achieve cooperative harmonization rather than homogenization, we propose CHARM, a novel complementary learning framework designed to implicitly align content while preserving modality-specific advantages through two components: (1) Mutual Perception Unit (MPU), enabling implicit alignment through window-based cross-modal interaction, where modalities serve as both queries and contexts for each other to discover modality-interactive correspondences; (2) A dual-path optimization strategy that decouples training into Collaborative Learning Strategy (CoL) for complementary fusion learning and Individual Enhancement Strategy (InE) for protected modality-specific optimization. Experiments across multiple datasets and backbones indicate that CHARM consistently outperform the baselines, with significant increment on the fragile modalities. This work shifts the focus from model homogenization to harmonization, enabling cross-modal complementarity for true harmony in diversity.