In this paper, we discuss performance modeling of 3-D stencil computing on an FPGA accelerator with a high-level synthesis environment, aiming for efficient exploration of user-space design parameters. First, we analyze resource utilization and performance to formulate these relationships as mathematical models. Then, in order to evaluate our proposed models, we implement heat conduction simulations as a benchmark application, by using MaxCompiler, which is a high-level synthesis tool for FPGAs, and MaxGenFD, which is a domain specific framework of the MaxCompiler for finite-difference equation solvers. The experimental results with various settings of architectural design parameters show the best combination of design parameters for pipeline structure can be systematically found by using our models. The effects of changing arithmetic accuracy and using data stream compression are also discussed.