Co-circulation of multiple influenza subtypes poses a major challenge to global public health. However, its specific impact on non-stationary epidemic sequences and coupling relationships with environmental drivers remains poorly understood. By integrating STL, Adaptive Fourier Decomposition, Continuous Wavelet Transform, and Wavelet Coherence, we analyzed 323 weekly influenza surveillance time series from China (2011–2025). The study identifies a fundamental regime shift during co-circulation periods, transitioning from ordered single-dominant transmission to a chaotic state. This instability is characterized by significant dominant periodicity dispersion, amplified seasonality shifts, and high-intensity anomalies in residual components, with overall seasonal strength dropping by 28%. Crucially, we uncover a marked north-south mechanistic divergence: northern regions exhibited “Environmental Locking,” remaining strongly constrained by climates during co-circulation; conversely, southern regions demonstrated “Environmental Decoupling” (H3N2 phase consistency with soil moisture plummeted from R=0.45 to 0.07), where viral ecological competition overshadowed environmental drivers. Influenza co-circulation acts as a systemic perturbation reshaping transmission dynamics. Our findings highlight the necessity for context-adaptive strategies: northern regions can maintain reliance on meteorological warnings, while southern regions must dynamically shift focus toward real-time virological surveillance during co-circulation to capture rapid ecological shifts.