Rolling bearings are important components in rotary machinery systems. In the field of multi-fault diagnosis of rolling bearings, the vibration signal collected from single channels tends to miss some fault characteristic information. Using multiple sensors to collect signals at different locations on the machine to obtain multivariate signal can remedy this problem. The adverse effect of a power imbalance between the various channels is inevitable, and unfavorable for multivariate signal processing. As a useful, multivariate signal processing method, Adaptive-projection has intrinsically transformed multivariate empirical mode decomposition (APIT-MEMD), and exhibits better performance than MEMD by adopting adaptive projection strategy in order to alleviate power imbalances. The filter bank properties of APIT-MEMD are also adopted to enable more accurate and stable intrinsic mode functions (IMFs), and to ease mode mixing problems in multi-fault frequency extractions. By aligning IMF sets into a third order tensor, high order singular value decomposition (HOSVD) can be employed to estimate the fault number. The fault correlation factor (FCF) analysis is used to conduct correlation analysis, in order to determine effective IMFs; the characteristic frequencies of multi-faults can then be extracted. Numerical simulations and the application of multi-fault situation can demonstrate that the proposed method is promising in multi-fault diagnoses of multivariate rolling bearing signal.