Seeding cells and scaffolds play pivotal roles in bone tissue engineering and regenerative medicine. Wharton's jelly-derived mesenchymal stem cells (WJCs) from human umbilical cord represent attractive and promising seeding cells in tissue regeneration and engineering for treatment applications. This study was carried out to explore the biocompatibility of scaffolds to seeding cells in vitro. Rod-like nano-hydroxyapatite (RN-HA) and flake-like micro-hydroxyapatite (FM-HA) coatings were prepared on Mg-Zn-Ca alloy substrates using micro-arc oxidation and electrochemical deposition. WJCs were utilized to investigate the cellular biocompatibility of Mg-Zn-Ca alloys after different surface modifications by observing the cell adhesion, morphology, proliferation, and osteoblastic differentiation. The in vitro results indicated that the RN-HA coating group was more suitable for cell proliferation and cell osteoblastic differentiation than the FM-HA group, demonstrating better biocompatibility. Our results suggested that the RN-HA coating on Mg-Zn-Ca alloy substrates might be of great potential in bone tissue engineering.