In this paper, the different discharge and polymerizing characteristics of Ar and He atmospheric pressure plasma jets (APPJs) were studied. The as-deposited polymer of acrylic acid (PAA) on silk fibroin film (SFF) by APPJs with Ar/O2 and He/O2 gases is investigated with AFM, FESEM and XPS. Optical emission spectroscopy (OES) measurements indicated that various reactive radicals, such as OH and O as well as some acrylic acid (AA) particles existed in the plasma jets. AFM images showed that the He/O2 plasma-deposited films had the most homogeneous characteristics and good water resistance properties. The cross-sections of silicon substrates obtained by FESEM showed that the deposition rates of PAA were 50 nm · min−1 and 15 nm · min−1 for Ar/O2 and He/O2 plasmas, respectively. Also, according to XPS analysis, He/O2 plasma created a higher concentration of carboxyl groups on the deposited film than when Ar/O2 plasma was used.