Channel estimation (CE) plays a key role in reconfigurable intelligent surface (RIS)-aided multiple-input multiple-output (MIMO) communication systems, while it poses a challenging task due to the passive nature of RIS and the cascaded channel structures. In this paper, a partially decoupled atomic norm minimization (PDANM) framework is proposed for CE of RIS-aided MIMO systems, which exploits the three-dimensional angular sparsity of the channel. In particular, PDANM partially decouples the differential angles at the RIS from other angles at the base station and user equipment, reducing the computational complexity compared with existing methods. A reweighted PDANM (RPDANM) algorithm is proposed to further improve CE accuracy, which iteratively refines CE through a specifically designed reweighing strategy. Building upon RPDANM, we propose an iterative approach named RPDANM with adaptive phase control (RPDANM-APC), which adaptively adjusts the RIS phases based on previously estimated channel parameters to facilitate CE, achieving superior CE accuracy while reducing training overhead. Numerical simulations demonstrate the superiority of our proposed approaches in terms of running time, CE accuracy, and training overhead. In particular, the RPDANM-APC approach can achieve higher CE accuracy than existing methods within less than 30 percent training overhead while reducing the running time by tens of times.