Nine physiological indicators of thirty-six macadamia varieties were determined under the prolonged drought stress, and the comprehensive analysis on drought resistance was conducted by using the subordination function method. It was showed that ‘YunMac 7’, ‘YunMac 24’, ‘YunMac 36’, ‘YunMac 32’ and ‘YunMac 17’ were the most drought-resistant varieties; ‘YunMac 29’, ‘YunMac 2’ and ‘YunMac 19’ the least drought-resistant varieties, and the other twenty-eight varieties were of the moderate drought resistance. In addition, correlations between the drought resistance and the nine physiological indicators were analyzed by using the gray connection analysis and the principal components analytic method. The result indicated that the leaf blade relative water content, the soluble sugar content, the soluble protein content, the superoxide dismutase and the free proline content could be treated as the important indicators of drought-resistant evaluation for the these macadamia varieties.