To describe the influence of different pecan seedling rootstocks on drought stress resistance, 12 rootstocks of ‘87MX1-2.2’, ‘87MX5-1.7’, ‘Elliott’, ‘Frutoso’, ‘Giles’, ‘Major’, ‘Moore’, ‘Peruque’, ‘Posey’, ‘Riverside’, ‘San Felipe’, and ‘VC1-68’ were selected as rootstock treatments for grafting. In addition, the experimental materials for the grafted young ‘Pawnee’ tree treatments included the pressure-volume technique (PV technique) and cutting shoot transpiration methods to plot the PV and the cutting shoot transpiration curves, and the parameters calculated from the two curves were used to analyze the data produced by the subordinate function and cluster dendrogram methods. The results revealed that the different seedling rootstock treatments influenced the ‘Pawnee’ grafted trees to varying degrees on aspects of drought resistance, the ability to save water, the modulation of osmosis, and the sensitivity of the stomatal response. The order of drought tolerance for these different pecan seedling rootstock treatments from high to low was as follows: ‘Posey’, ‘Peruque’, ‘Riverside’, ‘87MX5-1.7’, ‘VC1-68’, ‘Elliott’, ‘87MX1-2.2’, ‘San Felipe’, ‘Moore’, ‘Major’, ‘Giles’, and ‘Frutoso’.