Delimiting three lines (permanent basic farmland protection zones, urban growth boundaries and ecological protection redlines) scientifically is conducive to rational arrangement of land space resources and identifying the "three-line conflict" intensity factors can deepen the understanding of the national space planning. This study took the provincial spatial planning pilot area-Jiangxi province as an example, recognized the regional difference of "three-line conflict" by defining the "three-line conflict intensity", revealed its spatial characteristics by using spatial autocorrelation analysis, and analyzed the influencing factors of different types of conflict intensity by applying geographically weighted regression model (GWR). The results showed that the conflict areas of town-ecology, town-agriculture, ecology-agriculture and town-ecology-agriculture were 4305.791 km2, 2892.894 km2, 1845.341 km2 and 159.444 km2, respectively. There is obvious spatial clustering in the conflicts of town-ecology, town-agriculture, ecology-agriculture and town-ecology-agriculture. The main influencing factor of town-ecology conflict is the intensity of fixed assets investment, and the leading factor of town-agriculture conflict is the proportion of suitable area of construction land. The ecology-agriculture conflict is most affected by the topographic index, and the town-ecology-agriculture conflict is mainly affected by urbanization rate and the distance from river. The research results can provide reference for the rational layout of the "three lines" and the optimization of land structure.