Epitaxial oxide superlattices (SLs) of SrTiO3 (STO) and Nb-doped SrTiO3(STNO) were fabricated on LaAlO3 (LAO) (001) substrates by an ion beam sputter deposition (IBSD) system having double electron cyclotron resonance (ECR) ion guns. The [STOx/STNOy]10 SLs were epitaxially grown at different stacking sequences (x = 6 nm, y = 1–6 nm) and maintained the periodicity z of 10. Structural properties and surface morphology are found to be strongly dependent on the STNO sublayer thickness (y). Highly strained SLs with two-dimensional growth mode is observed at smaller STNO sublayer thickness (y = 1 nm). With increasing to a critical thickness (y = 4 nm), the SLs are freely strained and transformed to three-dimensional growth mode. The results demonstrate that the double ECR-IBSD is a versatile technique for the growth of high-quality oxide SLs.