Understanding ion diffusion mechanisms in layered materials is critical for advancing next-generation battery technologies. Using the well-characterized NaxCoO2 (NCO) system as a model platform, we investigated the temperature-dependent diffusion properties across a broad compositional range (x=0.33−0.89) using muon spin relaxation (μ+SR). Unexpected low-temperature internal magnetic field fluctuations were observed, systematically varying with Na content and appearing well before the onset of long-range diffusion. These fluctuations are attributed to phonon-assisted local Na motion, as suggested by a systematic increase in A with x, concurrent with a decreasing activation energy. The diffusion coefficient was calculated based on the crystal structure using a tailored diffusion model accounting for two inequivalent Na sites, yielding values consistent with those found in other layered battery materials. This work highlights the crucial role of phonon-coupled diffusion mechanisms in enabling ion transport at the microscopic scale, providing new insights into ion dynamics in layered solid-state conductors and their relevance to sodium-ion battery technology.