Nonbinary LDPC codes have shown superior performance close to the Shannon limit. Compared to binary LDPC codes of similar lengths, they can reach orders of magnitudes lower error rate. However, multitude of design freedoms of nonbinary LDPC codes complicates the practical code and decoder design process. Fast simulations are critically important to evaluate the pros and cons. Rapid prototyping on FPGA is attractive but takes significant design efforts due to its high design complexity. We propose a high-throughput reconfigurable hardware emulation architecture with decoder and peripheral co-design. The architecture enables a library and script-based framework that automates the construction of FPGA emulations. Code and decoder design parameters are programmed either during run time or by script in design time. We demonstrate the capability of the framework in evaluating practical code and decoder design by experimenting with two popular nonbinary LDPC codes, regular (2, dc) codes and quasi-cyclic codes: each emulation model can be auto-constructed within hours and the decoder delivers excellent error-correcting performance on a Xilinx Virtex-5 FPGA with throughput of up to hundreds of Mbps.