The present investigation explored the capability of priming treatment with 250 mg L−1 of humic acid (HA) to improve nano-ZnO tolerance of two rice cultivars seedlings (Zhu Liang You 06 and Qian You No. 1). The results showed that seed germination, seedling growth, total soluble protein, sugar and starch contents significantly improved by seed priming with HA especially under high nano-ZnO stress (500 and 750 mg L−1) as compared to unprimed seeds. In contrast, electrolyte leakage significantly increased after exposure to 500 and 750 mg L−1 nano-ZnO, but decreased obviously after HA priming in both cultivars. Abscisic acid (ABA) content in the seeds germinated under nano-ZnO stress was higher than those grown under non-stress condition; while gibberellins (GA) content decreased under nano-ZnO stress. HA priming down-regulated the relative expression levels of OsABA8ox2 and OsNCED1, which were key genes in ABA biosynthesis and catabolism of rice seeds. In contrast, up-regulation in OsGA20ox2 and OsGA3ox1 were induced by HA priming. The histochemical analysis reported that higher concentration of hydrogen peroxide (H2O2) and superoxide radical (O2·−) were observed in stressed roots with nano-ZnO as compared with non-stress condition, indicating reduction of root cell viability and severe oxidative burst. However, HA priming reduced obviously H2O2, O2·−, antioxidant enzymes activities (SOD, POD, CAT) and malondialdehyde (MDA) content of rice seedlings under stress. Significant increases in dehydroascorbate reductase (DHAR) and monodehydroascorbate reductase (MDAR) activities were observed in nano-ZnO stressed seedlings, but they were diminished evidently by HA priming. In addition, the improvement of HA on cell ultra structure of root tip and leaf mesophyll was detected under nano-ZnO stress especially 750 mg L−1 concentration. Therefore, it was suggested that HA priming could definitely improve the rice seed germination and seedling growth under nano-ZnO stress to some extent.