Human disturbance aggravates the evolution of ecosystem structure in the Yangtze River Delta (YRD) urban agglomeration, China which leads to the conflict between different ecosystem services (ESs). It is of great significance to clarify the trade-off intensity of ESs and its influencing factors in order to achieve the win-win goal of socioeconomic development and ecological protection. However, identification of the influencing factors and their underlying mechanisms in complex relationships among ESs remain under-researched. This study employed the YRD urban agglomeration as the study area and investigated the spatio-temporal changes of five key ESs in 2005 and 2019, such as carbon storage (CS), crop production (CP), habitat quality (HQ), water yield (WY) and nitrogen export (NE) by applying Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model. Spearman correlation analysis and Root Mean Square Error (RMSE) indicator were used for analyzing the trade-off intensity and their spatial pattern in the YRD urban agglomeration. Furthermore, redundancy analysis (RDA) method was used to reveal the key influencing factors of trade-off intensity. The results revealed that the amount of total carbon storage of the YRD urban agglomeration decreased by 1.17% from 2005 to 2019, the amount of total crop production increased by 30.18%, the amount of water yield increased by 87.92%, the amount of nitrogen export increased by 2.56%, and habitat quality decreased by 3.38%. In terms of spatial distribution, the high value areas of carbon storage, water yield and habitat quality were mainly concentrated in the southern area, while the total amount of crop production and nitrogen export in the northern region was higher. The spatial heterogeneity of trade-off intensity was significant, and the high values of trade-off intensity between CP-CS and CP-WY were mainly concentrated in the northern and the southern YRD urban agglomeration. The high values of trade-off intensity between NE-CS and CS-WY were mainly located in the southern region. The high values of trade-off intensity between CP-HQ and NE-HQ were mainly concentrated in the areas with rapid socio-economic development. The statistics of trade-off intensity showed that the overall trade-off intensity has increased from 2005 to 2019. The dynamics of ESs trade-off intensity in the YRD urban agglomeration was significantly affected by natural and socioeconomic factors, including slope, proportion of forestland, proportion of farmland, precipitation, temperature, proportion of construction land and so on. Slope, proportion of forestland and precipitation were negatively correlated with the trade-off intensity of NE-HQ, and positively correlated with other ESs pairs. The proportion of construction land, temperature, proportion of farmland and other factors were negatively correlated with the trade-off intensity of five ESs pairs except NE-HQ. Slope and proportion of forestland had a strongly positive correlation with CP-CS and CS-WY, but a strongly negative correlation with trade-off intensity of NE-HQ. The trade-off intensity of CP-CS was strongly correlated with proportion of construction land. The findings could improve the understanding of the spatiotemporal dynamics of trade-offs and their correlations with related factors.