In this paper, we investigate the problem of direction-of-arrival (DOA) estimation for massive multi-input multi-output (MIMO) radar, and propose a total array-based multiple signals classification (TA-MUSIC) algorithm for two-dimensional direction-of-arrival (DOA) estimation with a coprime cubic array (CCA). Unlike the conventional multiple signal classification (MUSIC) algorithm, the TA-MUSIC algorithm employs not only the auto-covariance matrix but also the mutual covariance matrix by stacking the received signals of two sub cubic arrays so that full degrees of freedom (DOFs) can be utilized. We verified that the phase ambiguity problem can be eliminated by employing the coprime property. Moreover, to achieve lower complexity, we explored the estimation of signal parameters via the rotational invariance technique (ESPRIT)-based multiple signal classification (E-MUSIC) algorithm, which uses a successive scheme to be computationally efficient. The Cramer–Rao bound (CRB) was taken as a theoretical benchmark for the lower boundary of the unbiased estimate. Finally, numerical simulations were conducted in order to demonstrate the effectiveness and superiority of the proposed algorithms.