Memristor-based processing-in-memory architecture is a promising solution to the memory bottleneck in the neural network ( NN ) processing. A major challenge for the programmability of such architectures is the automatic compilation of high-level NN workloads, from various operators to the memristor-based hardware that may provide programming interfaces with different granularities. This article proposes a source-to-source compilation framework for such memristor-based NN accelerators, which can conduct automatic detection and mapping of multiple NN operators based on the flexible and rich representation capability of the polyhedral model. In contrast to previous studies, it implements support for pipeline generation to exploit the parallelism in the NN loads to leverage hardware resources for higher efficiency. The evaluation based on synthetic kernels and NN benchmarks demonstrates that the proposed framework can reliably detect and map the target operators. Case studies on typical memristor-based architectures also show its generality over various architectural designs. The evaluation further demonstrates that compared with existing polyhedral-based compilation frameworks that do not support the pipelined execution, the performance can upgrade by an order of magnitude with the pipelined execution, which emphasizes the necessity of our improvement.