Linear time-distance helioseismic inversions are carried out for vector flow velocities using travel times measured from two ~1002 Mm2 × 20 Mm realistic magnetohydrodynamic quiet-Sun simulations of about 20 hr. The goal is to test current seismic methods on these state-of-the-art simulations. Using recent three-dimensional inversion schemes, we find that inverted horizontal flow maps correlate well with the simulations in the upper ~3 Mm of the domains for several filtering schemes, including phase-speed, ridge, and combined phase-speed and ridge measurements. In several cases, however, the velocity amplitudes from the inversions severely underestimate those of the simulations, possibly indicating nonlinearity of the forward problem. We also find that, while near-surface inversions of the vertical velocities are best using phase-speed filters, in almost all other example cases these flows are irretrievable due to noise, suggesting a need for statistical averaging to obtain better inferences.