The mesoporous silica wall materials can achieve controlled load and sustained-release of active agents. An antimicrobial nanoscale silica microcapsule containing cinnamaldehyde (CA) was prepared by the sol-gel method and applied in poly (butyleneadipate-co-terephthalate) (PBAT) film. The surface morphology, physical and chemical properties, and antibacterial properties of microcapsules and films were studied. The effects of different temperatures and humidities on the release behavior of microcapsules were also evaluated. Results showed that CA was successfully encapsulated in silica microcapsule which had a diameter of 450−700 nm. The antibacterial CA agent had a long-lasting release time under lower temperature and relative humidity (RH) environment. At low temperature (4 °C), the microcapsules released CA 32.35% in the first 18 h, and then slowly released to 56.08% in 216 h; however, the microcapsules released more than 70% in 18 h at 40 °C. At low humidity (50%RH), the release rates of microcapsules at the 18th h and 9th d were 43.04% and 78.01%, respectively, while it reached to equilibrium state at 72 h under 90% RH. The sustained release process of CA in SiO2-CA microcapsules follows a first-order kinetic model. Physicochemical properties of PBAT films loaded with different amounts of microcapsules were also characterized. Results showed that the tensile strength and water vapor transmission rate (WVTR) of the composite film containing 2.5% microcapsules were increased by 26.98% and 14.61%, respectively, compared to the raw film, while the light transmittance was slightly reduced. The crystallinity of the film was improved and can be kept stable up to 384.1 °C. Furthermore, microcapsules and composite film both exhibited distinctive antibacterial effect on Escherichia coli and Listeria monocytogenes. Therefore, SiO2-CA microcapsules and composite films could be a promising material for the active packaging.