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ABSTRACT We investigate the origin of photometric variability in the classical T Tauri star TW Hya by comparing light curves obtained by Transiting Exoplanet Survey Satellite (TESS) and ground-based telescopes with light curves created using three-dimensional (3D) magnetohydrodynamic (MHD) simulations. TW Hya is modelled as a rotating star with a dipole magnetic moment, which is slightly tilted about the rotational axis. We observed that for various model parameters, matter accretes in the unstable regime and produces multiple hotspots on the star’s surface, which leads to stochastic-looking light curves similar to the observed ones. Wavelet and Fourier spectra of observed and modelled light curves show multiple quasi-periodic oscillations (QPOs) with quasi-periods from less than 0.1 to 9 d. Models show that variation in the strength and tilt of the dipole magnetosphere leads to different periodograms, where the period of the star may dominate or be hidden. The amplitude of QPOs associated with the stellar period can be smaller than that of other QPOs if the tilt of the dipole magnetosphere is small and when the unstable regime is stronger. In models with small magnetospheres, the short-period QPOs associated with rotation of the inner disc dominate and can be mistaken for a stellar period. We show that longer period (5–9 d) QPOs can be caused by waves forming beyond the corotation radius.