Surfactants are often added to herbicidal formulations to improve the delivery of the herbicide into plants. In this study a new herbicidal formulation was formed based on the clopyralid with 0.01% gemini surfactant hexanediyl-1,6-bis(dimethylcetylammonium bromide) (16-6-16) as an adjuvant. The increase in the efficiency of the formulation was associated with the formation of a supramolecular surfactant–herbicide complex (SMC), which has improved wetting properties, provides high clopyralid concentration on the leaf surface, and has higher penetrating ability compared to surfactant-free clopyralid solutions. Comparison of the herbicidal action of clopyralid–16-6-16 SMC with two commercial formulations of the same concentration of clopyralid was performed using digital phenotyping of the model weed plant cocklebur (Xanthium strumarium). Based on the spectral indices NDVI (normalized differential vegetation index) and PSRI (plant senescence reflectance index) and key morphological indexes of the leaf angle, plant height, and leaf area, we showed that clopyralid formulations strongly affected the plants and that the strongest and most durable effect was exerted by the clopyralid–16-6-16 SMC formulation.