X-ray laser-induced structural changes in silicon undergoing femtosecond melting have been investigated by using an x-ray pump–x-ray probe technique. The experiment reveals that the atomic displacements start to increase at ∼20 fs after the intensity maximum of x-ray pump pulse. By comparing the observed time dependence of the atomic disordering and the dedicated theoretical simulations, we interpret that the energy transfer from the excited electrons to ions via electron-ion coupling (thermal effect) as well as a strong modification of the interatomic potential due to electron excitations (nonthermal effect) trigger the ultrafast atomic disordering. Our results highlight the need to consider the interplay of thermal and nonthermal effects in the quantitative modeling of the interaction of intense x rays with matter.