Architecture reverse engineering has become an emerging attack against deep neural network (DNN) implementations. Several prior works have utilized side-channel leakage to recover the model architecture while the target is executing on a hardware acceleration platform. In this work, we target an open-source deep-learning accelerator, Versatile Tensor Accelerator (VTA), and utilize electromagnetic (EM) side-channel leakage to comprehensively learn the association between DNN architecture configurations and EM emanations. We also consider the holistic system -- including the low-level tensor program code of the VTA accelerator on a Xilinx FPGA and explore the effect of such low-level configurations on the EM leakage. Our study demonstrates that both the optimization and configuration of tensor programs will affect the EM side-channel leakage. Gaining knowledge of the association between the low-level tensor program and the EM emanations, we propose NNReArch, a lightweight tensor program scheduling framework against side-channel-based DNN model architecture reverse engineering. Specifically, NNReArch targets reshaping the EM traces of different DNN operators, through scheduling the tensor program execution of the DNN model so as to confuse the adversary. NNReArch is a comprehensive protection framework supporting two modes, a balanced mode that strikes a balance between the DNN model confidentiality and execution performance, and a secure mode where the most secure setting is chosen. We implement and evaluate the proposed framework on the open-source VTA with state-of-the-art DNN architectures. The experimental results demonstrate that NNReArch can efficiently enhance the model architecture security with a small performance overhead. In addition, the proposed obfuscation technique makes reverse engineering of the DNN architecture significantly harder.