Decellularized tendon matrix (DTM) has shown great potential for inducing tenogenic differentiation and facilitating tendon repair. In which, the retained native tendon-derived matrix in DTM is considered as the main factor for these effects. However, whether preservation of the highly aligned architecture of DTM is also essential for tenogenic differentiation and tendon repair has not been well investigated yet. In this study, we prepared aligned DTM (A-DTM), in which the native aligned architecture was preserved and random DTM (R-DTM), in which the native architecture was disrupted. In vitro study indicated that after decellularization procedures, both A- and R-DTM retained most of the tendon extracellular matrix (ECM). In addition, A-DTM exhibited an inherent aligned architecture, whilst, R-DTM showed a random arranged surface topography. Both DTM materials exhibited good biocompatibility for tendon stem/progenitor cells (TSPCs) and adipose stem cells (ASCs). They were able to adhere and proliferate on the DTM materials and maintain high viability. Interestingly, A-DTM promoted longitudinally oriented growth pattern of TSPCs and ASCs, whereas, cells grown on the R-DTM showed a random spreading. Furthermore, both DTM materials induced tenogenic differentiation of TSPCs and ASCs without the addition of any exotic growth factors. However, A-DTM demonstrated a stronger pro-tendon differentiation compared to R-DTM. In vivo study demonstrated that A-DTM combined with TSPCs or ASCs significantly promoted functional repair of injured Achilles tendon while reducing fibrovascular scar and heterotopic ossification (HO) formation. Taken together, these results indicated that aligned architecture of DTM is essential for stem cell tenogenic differentiation and tendon repair. Thus, for the application of DTM, it is very important to preserve its native aligned architecture. In another scenario, when DTM was used to prepared a composite biomaterial, a tendon-mimic topography should be re-constructed.