In the present study, nanoliposomes composed of rapeseed lecithin were used for the encapsulation of anthocyanin compounds (AC). The nanoliposomes were prepared using hydration and ultrasound combined method, and the effect of AC concentration (4.5, 6.75, 9% w/w) on the characteristics of nanoliposomes including particle size, polydispersity index (PDI), zeta potential, and the encapsulation efficiency (EE) of nanoliposomes with and without AC were studied. The results suggested the fabricated nanoliposomes had a size range of 141–196 nm, negative zeta potential and narrow particle size distribution. Further, the samples containing 9% extract had the maximum EE (43%). The results showed elevation of AC concentration resulted in increased particle size, PDI, EE, and surface charge of nanoparticles. The presence of AC extract led to diminished membrane fluidity through the hydrophobic interactions with the hydrocarbon chain of fatty acids. TEM images suggested that the nanoliposomes were nearly spherical and the AC caused their improved sphericity. Further, in vitro biocompatibility tests for human mesenchymal (MSC) and fibroblast (FBL) cells indicated nanoparticles were not toxic. Specifically, the best formulations with the maximum compatibility and bioavailability for MSC and FBL cells were AC-loaded nanoliposomes with concentrations of 0.5 mL/mg and 10.3 mL/µg and, respectively.