In this study, an oral self-micro-emulsifying drug delivery system of honokiol (HN-SMEDDS) was developed to overcome honokiol's disadvantages, such as poor aqueous solubility and induced stress responses. The safeties of HN-SMEDDS and honokiol dimethyl sulfoxide aqueous solution (HN-DMSO) were evaluated by comparing their hemolytic activity and acute toxicity in pompano (Trachinotus ovatus). The one-h-ten-percent hemolytic concentration (EC10) of HN-SMEDDS on pompano erythrocytes was 1.206 mg/mL, 33.5 times that of HN-DMSO. And the minimum lethal doses (MLD) for HN-SMEDDS and HN-DMSO in pompano were 1000 mg/kg and 500 mg/kg, respectively. The 14-d relative percent survival (RPS) was calculated after orally administering substance HN-SMEDDS at various doses in pompano cryptocaryoniasis, revealing an optimal dose of 400 mg/kg. To assess efficacy, a comparison was carried out between the oral administration of HN-SMEDDS and HN-DMSO in treating pompano cryptocaryoniasis. This comparison was based on the 14-d RPS and the quantification of C. irritans trophonts in the right second gill (NCTG). In the challenged pompanos treated with HN-SMEDDS and HN-DMSO, the 14-d RPS and 7-d NCTG reached 68.89 ± 3.14% and 6.3 ± 2.1 individuals, and 53.33 ± 0.00% and 30.7 ± 2.1 individuals, respectively. Furthermore, stress-related markers, encompassing mRNA levels of cyp1a, hsp70, gst, and sod in the liver, spleen, and kidney, along with activities of ACP, CAT, SOD, GSH, and T-AOC in these organs and serum, were compared between the pompanos administered with HN-SMEDDS and HN-DMSO. The impact of HN-SMEDDS on the mRNA levels of cyp1a in the liver and kidney, hsp70 in all the analyzed tissues, gst in the liver and spleen, sod in the spleen, as well as the activities of ACP and CAT in liver, spleen, and serum, GSH content in spleen and kidney, SOD in the liver, kidney, and serum, and the T-AOC in liver, spleen, kidney, and serum, were significantly smaller than those of HN-DMSO. Compared to HN-DMSO, HN-SMEDDS could markedly reduce the stress responses of fish and enhance the efficacy of honokiol.