Osteoblast differentiation can be modulated by variations in order of nanoscale topography. Biopolymers embedded with carbon nanotubes can cause various orders of roughness at the nanoscale and can be used to investigate the dynamics of extracellular matrix interaction with cells. In this study, clear relationship between the response of osteoblasts to integrin receptor activation, their phenotype, and transcription of certain genes on polymer composites embedded with carbon nanotubes was demonstrated. We generated an ultrathin nanocomposite film embedded with carbon nanotubes and observed improved adhesion of pre-osteoblasts, with a subsequent increase in their proliferation. The expression of genes encoding integrin subunits α5, αv, β1, and β3 was significantly upregulated at the early of time-point when cells initially attached to the carbon nanotube/polymer composite. The advantage of ultrathin nanocomposite film for pre-osteoblasts was demonstrated by staining for the cytoskeletal protein vinculin and cell nuclei. The expression of essential transcription factors for osteoblastogenesis, such as Runx2 and Sp7 transcription factor 7 (known as osterix), was upregulated after 7 days. Consequently, the expression of genes that determine osteoblast phenotype, such as alkaline phosphatase, type I collagen, and osteocalcin, was accelerated on carbon nanotube embedded polymer matrix after 14 days. In conclusion, the ultrathin nanocomposite film generated various orders of nanoscale topography that triggered processes related to osteoblast bone formation.