Understanding the electrokinetic conversion efficiency in a nanochannel is vital for designing energy storage and conversion devices. In this paper, an analytical electrokinetic energy conversion efficiency in a nanochannel is obtained based on the linear electrokinetic response. The analytical result shows that the conversion efficiency has a maximum with the increasing of the nanochannel pore radius. Numerical solutions based on the Poisson-Nernst-Planck (PNP) and Navier-Stokes (NS) equations are used to con-firm the analytical expressions. Besides, the influences of the pore radius and surface roughness on the conversion efficiency in nanochannels are also studied by the numerical calculations. In particular, the influences of the surface roughness on the fluid flow, streaming current and streaming potential are examined. The results show that the large bumps and grooves representing the roughness can hinder the fluid flows and ion transports in the nanochannels. The maximum efficiency in a smooth nanochannel is higher than that in a rough channel. However, the small bumps and grooves can increase the surface area of the channel, which is beneficial to improving the conversion efficiency in some cases. This research can provide theoretical guidance to design electrokinetic energy conversion devices.