Abstract: Territory is the basis of all economic and social activity. Exploring the spatial-temporal characteristics and influencing factors of eco-efficiency is of great significance to the sustainable utilization of territory resources, as well as to economic and social development. Based on the Three-Zone Space perspective and multi-source data, the Territory Use Eco-Efficiency (TUEE) measurement system was constructed. The Undesirable Super-SBM model, spatial autocorrelation analysis and multi-scale geographically weighted regression (MGWR) were used in this study to analyze TUEE levels, spatial-temporal differences, and the driving factors in 53 counties in Jiangsu Province from 2000 to 2020. The results showed that: (1) the TUEE level of Jiangsu Province generally showed a gradual upward trend during the surveyed period. The urban space and ecological space eco-efficiency were steadily improved, while the agricultural space eco-efficiency decreased at first but then increased; (2) Jiangsu Province was in the procedure of changing from a scattered distribution of counties with high TUEE levels, to a pattern of high-TUEE counties in the south and low-TUEE levels in the north. The TUEE in coastal counties had certain advantages over inland counties. During the study period, there was a significant spatial positive correlation, and the correlation was increasing. High-high agglomeration was distributed in southern Jiangsu counties, and the low-low agglomeration was distributed in northern counties. (3) There was spatial heterogeneity in the influencing factors of TUEE levels in the province. Temperature and level of openness to the outside world had a significant promoting effect, while elevation had a significant inhibitory effect. Population density and level of economic development also had a promoting effect, but it was not statistically significant. Based on these findings, in order to enhance the overall TUEE of Jiangsu Province, it is necessary to strengthen inter-county connections, carry out territory utilization activities according to local conditions, optimize industrial structures and government investment structures.