This study is focused on the preparation, characterization, and multifunctional properties of intelligent hybrid nanopigments. The hybrid nanopigments with excellent environmental stability and antibacterial and antioxidant properties were fabricated based on naturalMonascusred, surfactant, and sepiolite via a facile one-step grinding process. The density functional theory calculations demonstrated that the surfactants loaded on sepiolite were in favor of enhancing the electrostatic, coordination, and hydrogen bonding interactions betweenMonascusred and sepiolite. Thus, the obtained hybrid nanopigments exhibited excellent antibacterial and antioxidant properties, with an inhibition effect on Gram-positive bacteria that was superior to that of Gram-negative bacteria. In addition, the scavenging activity on DPPH and hydroxyl free radicals as well as the reducing power of hybrid nanopigments were higher than those of hybrid nanopigments prepared without the addition of the surfactant. Inspired by nature, gas-sensitive reversible alochroic superamphiphobic coatings with excellent thermal and chemical stability were successfully designed by combining hybrid nanopigments and fluorinated polysiloxane. Therefore, intelligent multifunctional hybrid nanopigments have great application foreground in related fields.