Adaptive control can use hierarchical motion estimation (HME) and/or multiple reference motion estimation (MRME) for the motion estimation of current encoding blocks. Both HME and MRME are allowed in the motion estimation to achieve a high coding gain. Control consists of slice level control and macro-block (MB) level control. A slice is one or more contiguous macroblocks. In slice level control, it is decided to use only one reference frame or use multiple reference frames to coding current slice based on the motion vectors obtained in coarse level motion estimation. In MB level control, it is decided to perform MRME or perform HME for the MB and its subblocks based on the coarse level motion vectors of the MB.