Derived from multiple sources of high-resolution data that covered a time span from mid-2003 until early 2020, this dataset consists of dinoflagellate cysts (dinocysts) export flux time series obtained by a Honjo-type sediment trap offshore Cape Blanc and key environmental factors time series in the Canary Current upwelling ecosystem, Northwest Africa. The dinocyst time series comprises absolute abundances of all identified dinocyst taxa and four main groups showcasing particular ecological signals. Meanwhile, the time series of environmental factors originated from land observations (Nouadibhou Airport) of dust storm activity, surface wind speed, and surface wind direction, as well as satellite-based observations of aerosol dust frequency, sea surface temperature, and sea surface temperature anomaly. The resolution of each time series was standardised, and new time series were interpolated to meet the requirement of wavelet time series analysis, which could determine the common cyclical patterns in the time series of dinocysts and environmental factors. This approach aimed to distinguish climatic-driven changes by linking the interannual variations that occurred in environments and the dinocyst export flux cycles.