The rapid urbanization process has severely affected the ecological security and ecosystem services (ESs) in China’s southern province of Fujian, and threated the sustainable development of the local economy and society in the last two decades. This study mapped the spatial-temporal variation of four types of ESs and evaluated the tradeoffs/synergies among the ESs in Fujian Province from 2000 to 2020 on the three scales of the province, city and county. The results showed that: (1) From 2000 to 2020, the three ESs functions of soil conservation service, carbon storage service, and habitat quality decreased, while the function of food supply service increased. (2) At the provincial scale, soil conservation services, carbon storage services, and habitat quality were in a synergistic relationship, and food supply service was always in tradeoffs relationships with soil conservation services, carbon storage services, and habitat quality. At the prefecture-level scale, the tradeoffs/synergies among ESs vary among prefecture-level cities. At the county scale, the Moran’s I index of bivariate spatial autocorrelation was consistent with the correlation coefficient, and the tradeoffs/synergies between ESs showed significant spatial heterogeneity. (3) Based on the correlation analysis method, the Ecosystem Service Tradeoff-synergy Degree (ESTD) model and bivariate spatial autocorrelation analysis can clearly show the relationship between various ESs, and the research results are relatively consistent. The spatial distribution of four ecosystem services in Fujian province showed a specific aggregation pattern. High—high concentrations and low—low concentrations are strong. Low—high agglomeration and high—low agglomeration are weak.