Biodegradable polymer-based nanocomposite coatings provide multiple advantages to modulate the corrosion resistance and cytocompatibility of magnesium (Mg) alloys for biomedical applications. Biodegradable poly(glycerol sebacate) (PGS) is a promising candidate used for medical implant applications. In this study, we synthesized a new PGS nanocomposite system consisting of hydroxyapatite (HA) and magnesium oxide (MgO) nanoparticles and developed a spray coating process to produce the PGS nanocomposite layer on pretreated Mg substrates, which improved the coating adhesion at the interface and their cytocompatibility with bone marrow derived mesenchymal stem cells (BMSCs). Prior to the spray coating process of polymer-based nanocomposites, the Mg substrates were pretreated in alkaline solutions to enhance the interfacial adhesion strength of the polymer-based nanocomposite coatings. The addition of HA and MgO nanoparticles (nHA and nMgO) to the PGS matrix, as well as the alkaline pretreatment of the Mg substrates, significantly enhanced the interfacial adhesion strength when compared with the PGS coating on the nontreated Mg control. The average BMSC adhesion densities were higher on the PGS/nHA/nMgO coated Mg than the noncoated Mg controls under direct contact conditions. Moreover, the addition of nHA and nMgO to the PGS matrix and coating the nanocomposite onto Mg substrates increased the average BMSC adhesion density when compared with the PGS/nHA/nMgO coated titanium (Ti) and PGS coated Mg controls under direct contact. Therefore, the spray coating process of PGS/nHA/nMgO nanocomposites on Mg substrates or other biodegradable metal substrates could provide a promising surface treatment strategy for biodegradable implant applications.