Leaf indexes of six sea buckthorn varieties were analyzed based on paraffin section for the purpose of investigating drought resistance, including the cuticle thickness of leaves, upper and lower epidermis thickness, palisade tissue thickness, thickness of spongy tissue, leaf thickness, ration of palisade/spongy, tightness and looseness of leaf tissue structure, etc. Our results indicated that the foregoing indexes showed conspicuous drought resistant, and significant difference existed between male and female individuals respectively. The female cuticle thickness and palisade tissue thickness varied largely while the male palisade tissue thickness, thickness of spongy tissue and leaf thickness had relatively high coefficients of variation, all above 20%. The female palisade tissue thickness, upper and lower epidermis thickness, thickness of spongy tissue and tissue structure loose ratio (SR) were selected to evaluate the water control capability of six sea buckthorn varieties comprehensively according to subordinate function value method. The order of drought resistance for six female sea buckthorn was Hunjin Qiuyisike × Zhongguoshaji Zhongguoshaji Chuyi Taiyang Wulangemu× Zhongguoshaji. Leaf tissue structure tense ratio (CTR), lower epidermis thickness, thickness of palisade tissue and SR were selected as male drought resistance indexes, and the order of drought resistance for male sea buckthorn was Qiuyisike ×Zhongguoshaji Chuyi Wulangemu×Zhongguoshaji Hunjin Zhongguoshaji.