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The size effects that reveal the dramatic changes of mechanical behaviour at nanoscales have traditionally been analysed for regular beam systems. Here, the method of using finite-element analysis is explored with the intention of evaluating the size effects for complex nanostructures. The surface elasticity theory and generalized Young–Laplace equation are integrated into a beam element to account for the size effects in classical Euler–Bernoulli and Timoshenko beam theories. Computational results match well with the theoretical predictions on the size effect for a cantilever beam and a cubic unit cell containing 24 horizontal/vertical ligaments. For a simply supported nanowire, it is found that the results are very close to the experimental data. With the assumption that nanoporous gold is composed of many randomly connected beams, for the first time, the size effect of such a complex structure is numerically determined.