Memristor-based neuromorphic computing system provides a promising solution to significantly boost the power efficiency of computing system. Memristor-based neuromorphic computing system has a wide range of design choices, such as the various memristor crossbar cell designs and different parallelism degrees of peripheral circuits. However, a memristor-based neuromorphic computing system simulator, which is able to model the system and realize an early-stage design space exploration, is still missing. In this paper, we develop a memristor-based neuromorphic system simulation platform (MNSIM). MNSIM proposes a general hierarchical structure for memristor-based neuromophic computing system, and provides flexible interface for users to customize the design. MNSIM also provides a detailed reference design for large-scale applications. MNSIM embeds estimation models of area, power, and latency to simulate the performance of system. To estimate the computing accuracy, MNSIM proposes a behavior-level model between computing error rate and crossbar design parameters considering the influence of interconnect lines and non-ideal device factors. The error rate between our accuracy model and SPICE simulation result is less than 1%. Experimental results show that MNSIM achieves more than 7000 times speed-up compared with SPICE and obtains reasonable accuracy. MNSIM can further estimate the trade-off between computing accuracy, energy, latency, and area among different designs for optimization.