Dynamic CT myocardial perfusion imaging (DCT-MPI) is a reliable examination tool for the assessment of myocardium and vascular, while its special scan protocol may result in excessive radiation exposure to patients and inevitable inter-frame motion. Lowering the tube current is a simple way to reduce radiation exposure. However, low mAs will certainly cause severe image noise, thus may further impact the accuracy of functional hemodynamic parameters, which are used for the assessment of blood supply. In this work, we present a novel scheme applying motion compensation and local low rank regularization (MC-LLR) for obtaining high quality motion compensated DCT-MPI images. Specifically, motion compensation by using robust data decomposition registration (RDDR) was introduced. Robust principal component analysis coupled with optical flow-based registration algorithm were used in RDDR. Then, the local low rank constraint on the motion compensated time series images was applied for the DCT-MPI reconstruction. One healthy mini pig and two patient datasets were used to evaluate the proposed MC-LLR algorithm. Results show that the present method achieved satisfactory image quality with higher CNRs, smaller rRMSEs, and more accurate hemodynamic parameter maps.