In this study, we present a novel surface model that utilizes surface energy density to predict the surface effect in nanobeam contact problems. To address the issue of a finite-length elastic nanobeam being indented by a rigid cylindrical indenter, we propose an equivalent substitution method. This method allows us to formulate analytical relations between the load and contact half-width for two different boundary cases. The explicit expressions of the contact-zone width, the pressure distribution in the contact zone, the deflection outside the contact zone, and the load–displacement relation are obtained for the nanobeam with surface effect and are compared with classical results in detail. The results show that the influence of the surface effect is very significant for nanobeam contact behavior, especially when the half-width of the contact zone increases and the contact zone becomes two independent symmetric strips. It is also found that the length-height ratio of nanobeam and the end support conditions have a fairly obvious effect on the normalized pressure distribution, which deviates significantly from the one predicted by the classical results due to the surface effect. However, for a given beam length and indenter radius, the ratio of the width of the contact zone to the beam thickness is almost constant, independent of the indenter load and beam boundary conditions. Meanwhile, the model predicts that the contact pressure distribution after the normalization of the average indentation pressure is almost independent of the indentation load and beam boundary conditions, but obviously depends on the surface effect parameters. The present method and result should be helpful not only to the measurement of mechanical properties of the indentation nanobeam but also to the design of the nanobeam-based devices.