In this article, we propose a programmable plasmonic waveguide system (PPWS) to achieve several different functions based on metal coding metamaterials (MCMs) and inverse design technology. There is no need to spend much time on considering the relation between the function and the structure because the MCMs in the PPWS are reprogrammable. In order to demonstrate the effectiveness of the PPWS, we utilize it to achieve several filtering functions, including bandstop and bandpass filters. The simulation results exhibit that the performance of filters is improved based on genetic algorithm, particle swarm optimization, multi-traversal direct-binary search and simulated annealing. Especially, the bandwidth and quality factor for the narrow-band filter can reach 6.5 nm and 200.5. In addition to the simple filtering functions, some relatively complex transmission characteristics can be obtained by using the PPWS, such as plasmon-induced transparency-like effects. In conclusion, genetic algorithm is considered as the most efficient inverse design method for our system due to its less optimization time and stable performance. In comparison with the previous works, our proposed PPWS not only provides a general framework for obtaining an effective, flexible and compact plasmonic device but also shows the applications of inverse design on photonics devices.