The first measurement of longitudinal decorrelations of harmonic flow amplitudes \(v_n\) for \(n=2\), 3 and 4 in Xe+Xe collisions at \(\sqrt{s_{\mathrm{NN}}}=5.44\) TeV is obtained using 3~\({\mu}\textrm{b}^{-1}\) of data with the ATLAS detector at the LHC. The decorrelation signal for \(v_3\) and \(v_4\) is found to be nearly independent of collision centrality and transverse momentum (\(p_{\mathrm{T}}\)) requirements on final-state particles, but for \(v_2\) a strong centrality and \(p_{\mathrm{T}}\) dependence is seen. When compared with the results from Pb+Pb collisions at \(\sqrt{s_{\mathrm{NN}}}=5.02\) TeV, the longitudinal decorrelation signal in mid-central Xe+Xe collisions is found to be larger for \(v_2\), but smaller for \(v_3\). Current hydrodynamic models reproduce the ratios of the \(v_n\) measured in Xe+Xe collisions to those in Pb+Pb collisions but fail to describe the magnitudes and trends of the ratios of longitudinal flow decorrelations between Xe+Xe and Pb+Pb. These results provide new insights into the longitudinal structure of the initial-state geometry in heavy-ion collisions.