In this paper, the weighted estimates for multilinear pseudo-differential operators were systematically studied in rearrangement invariant Banach and quasi-Banach spaces. These spaces contain the Lebesgue space, the classical Lorentz space and Marcinkiewicz space as typical examples. More precisely, the weighted boundedness and weighted modular estimates, including the weak endpoint case, were established for multilinear pseudo-differential operators and their commutators. As applications, we show that the above results also hold for the multilinear Fourier multipliers, multilinear square functions, and a class of multilinear Calderón-Zygmund operators.