Sodar (SOund Detection And Ranging), eddy-covariance, and tower profile measurements of wind speed and carbon dioxide were performed during 17 consecutive nights in complex terrain in northern Taiwan. The scope of the study was to identify the causes for intermittent turbulence events and to analyze their importance in nocturnal atmosphere–biosphere exchange as quantified with eddy-covariance measurements. If intermittency occurs frequently at a measurement site, then this process needs to be quantified in order to achieve reliable values for ecosystem characteristics such as net ecosystem exchange or net primary production. Fourteen events of intermittent turbulence were identified and classified into above-canopy drainage flows (ACDFs) and low-level jets (LLJs) according to the height of the wind speed maximum. Intermittent turbulence periods lasted between 30 and 110 min. Towards the end of LLJ or ACDF events, positive vertical wind velocities and, in some cases, upslope flows occurred, counteracting the general flow regime at nighttime. The observations suggest that the LLJs and ACDFs penetrate deep into the cold air pool in the valley, where they experience strong buoyancy due to density differences, resulting in either upslope flows or upward vertical winds. Turbulence was found to be stronger and better developed during LLJs and ACDFs, with eddy-covariance data presenting higher quality. This was particularly indicated by spectral analysis of the vertical wind velocity and the steady-state test for the time series of the vertical wind velocity in combination with the horizontal wind component, the temperature, and carbon dioxide. Significantly higher fluxes of sensible heat, latent heat, and shear stress occurred during these periods. During LLJs and ACDFs, fluxes of sensible heat, latent heat, and CO2 were mostly one-directional. For example, exclusively negative sensible heat fluxes occurred while intermittent turbulence was present. Latent heat fluxes were mostly positive during LLJs and ACDFs, with a median value of 34 W m−2, while outside these periods the median was 2 W m−2. In conclusion, intermittent turbulence periods exhibit a strong impact on nocturnal energy and mass fluxes.