Low clouds significantly influence Earth’s radiation budget, but their climate feedback remains highly uncertain due to complex interactions with meteorological conditions across spatial and temporal scales. The cloud controlling factor framework is widely used to link meteorological variables with cloud properties. However, most studies assume a static, linear relationship, potentially obscuring the timescale-dependent responses. In this study, we apply the Ensemble Empirical Mode Decomposition method to ISCCP-H cloud observations and ERA5 data (1987–2016) to isolate low cloud amount across multiple intrinsic timescales and trends over global land and ocean. The trends show a nonlinear increase in stratocumulus (Sc) and a significant nonlinear decline in cumulus (Cu), while stratus (St) exhibits weaker trends. We categorize timescales short (≤1 year) for annual variations, medium (1–8 years) for interannual variability such as ENSO, and long (>8 years) for decadal and longer-term climate changes. It is found that Sc and Cu over land are primarily influenced by near-surface heating, while sea surface temperature and surface sensible heat flux (SHF) dominate over ocean at short timescales. SHF becomes dominant over land at medium timescales, largely reflecting ENSO-related induced surface anomalies. At long timescales, atmospheric stability and wind speed influence continental clouds, while SHF remains dominant over ocean. Trend components reveal that Sc and Cu are most sensitive to temperature changes, whereas St responds to mid-level humidity over ocean and SHF over land. These findings underscore the importance of timescale-dependent cloud–meteorology relationships to improve cloud parameterizations and reduce climate projection uncertainties. Overall, our results demonstrate that low cloud variability and trends cannot be explained by a single linear mechanism but instead arise from distinct meteorological controls that change across timescales, cloud types, and surface regimes.