Memristor based neuromorphic computing systems give alternative solutions to boost the computing energy efficiency of Neural Network (NN) algorithms. Because of the large-scale applications and the large architecture design space, many factors will affect the computing accuracy and system's performance. In this work, we propose a behavior-level modeling tool for memristor-based neuromorphic computing systems, MNSIM 2.0, to model the performance and help researchers to realize an early-stage design space exploration. Compared with the former version and other benchmarks, MNSIM 2.0 has the following new features: 1. In the algorithm level, MNSIM 2.0 supports the inference accuracy simulation for mixed-precision NNs considering non-ideal factors. 2. In the architecture level, a hierarchical modeling structure for PIM systems is proposed. Users can customize their designs from the aspects of devices, interfaces, processing units, buffer designs, and interconnections. 3. Two hardware-aware algorithm optimization methods are integrated in MNSIM 2.0 to realize software-hardware co-optimization.