The submitochondria location of a mitochondrial protein is very important for further understanding the structure and function of this protein. Hence, it is of great practical significance to develop an automated and reliable method for timely identifying the submitochondria locations of novel mitochondrial proteins. In this study, a sequence-based algorithm combining the augmented Chou's pseudo amino acid composition (Chou's PseAA) based on auto covariance (AC) is developed to predict protein submitochondria locations and membrane protein types in mitochondria inner membrane. The model fully considers the sequence-order effects between residues a certain distance apart in the sequence by AC combined with eight representative descriptors for both common proteins and membrane proteins. As a result of jackknife cross-validation tests, the method for submitochondria location prediction yields the accuracies of 91.8%, 96.4% and 66.1% for inner membrane, matrix, and outer membrane, respectively. The total accuracy is 89.7%. When predicting membrane protein types in mitochondria inner membrane, the method achieves the prediction performance with the accuracies of 98.4%, 64.3% and 86.7% for multi-pass inner membrane, single-pass inner membrane, and matrix side inner membrane, where the total accuracy is 93.6%. The overall performance of our method is better than the achievements of the previous studies. So our method can be an effective supplementary tool for future proteomics studies. The prediction software and all data sets used in this article are freely available at http://chemlab.scu.edu.cn/Predict_subMITO/index.htm.