Exploring the dynamic variation in ecosystem services and clarifying the driving mechanism will help with the formulation of effective ecological environment protection policies. Accordingly, this study sought to reveal the complex variability in ecosystem services in the Yellow River Delta (YRD) at a higher temporal resolution and the transition between the main driving factors in different periods. To this end, we used the economic equivalent factor valuation method to quantify the ecosystem service value from 2000 to 2019 at 5-year intervals. Furthermore, the Geo-detector model was used to identify the main driving factors and interaction between the driving factors of ecosystem service value variations. Then, we analyzed the temporal and spatial dynamic variations in the ecosystem service value and the transitions between the main driving factors in different periods. The main results are as follows: (1) From 2000 to 2019, the ecosystem service value of the YRD showed an increasing trend followed by a decline, whereby water and construction land increased and the other classes of land decreased. Overall, the inland and coastal distribution patterns exhibited low and high values, respectively. (2) The main driving factors of ecosystem service value variations were the NDVI and topographical factors (aspect, slope, elevation), which had q values that were stable and greater than those of the other factors. Although human activity, tourist resource concentration and traffic convenience factors had a comparatively minor effect on ecosystem services, we noted a trend where their effects increased from 2000 to 2019. (3) The detection of interactions revealed complex mechanisms affecting the variation in the YRD. Interactions between variables had a stronger influence than individual effects. The interactions between the Normalized Difference Vegetation Index (NDVI) and other factors consistently had the most significant impact. These interactions primarily shaped the spatial and temporal distribution of ecosystem services. The NDVI and human activities exhibited nonlinear enhancement. These results contribute to improving our cognition of the factors and mechanisms influencing ecosystem services, offering theoretical support for the improvement of ecosystem services in the YRD.