Introduction The hormone Fibroblast Growth Factor 21 (FGF21), as a novel glucose and lipid metabolism regulator, has become a promising therapeutic target for metabolic disorders. Camel, the characteristic species adapted to arid and semi-arid desert climates, has shown exceptional ability for the regulation of lipid reserve and utilization.Methods This study found camel FGF21 to have a stronger regulatory effect for downstream signaling compared to human and mouse through sequence analysis and FGF21 signal downstream markers detection. FGF21 protein has been found to have one potential drug-binding pocket, which has been predicted using the CavityPlus online platform. Four small compounds, resorcinol monoacetate, tropisetron, nylidrin, and stiripentol, targeting FGF21 protein have been screened by molecular docking using the UCSF DOCK6 program.Results The inhibitory concentration 50% (IC50) values of the four small compounds have been determined by MTT assay and the values have been simulated by the software GraphPad Prism. The biological effect testing has indicated the four compounds to be involved in the regulation of the FGF21 signaling pathway and serve as agonists for FGF21 signaling transduction. While the blocking experiment of compound and protein co-treatment has indicated the four small compounds to not inhibit FGF21-induced pathway activation. Even, resorcinol monoacetate and stiripentol have shown to synergistically activate downstream signaling pathways with the FGF21 protein.Conclusion This study has provided new ideas for developing therapeutic strategies based on FGF21 protein modification and exploring novel disease treatment strategies based on the compounds-protein combination.