In aerospace application, computational fluid dynamics (CFD) is recognized as a cost effective design tool. UPACS, a package for CFD is convenient for users, which has various solvers to support large scale of complexity. The problem is its computation speed which is hard to be enhanced by using clusters due to its complex memory access patterns. As an economical solution, accelerators using FPGAs are hopeful candidates. However, the total scale of UPACS is too large to be implemented on small numbers of FPGAs. For cost efficient implementation, partial reconfiguration which can dynamically reconfigure only required functions is proposed in this paper. MUSCL scheme, a main function used frequently in UPACS is selected as a target. Partial reconfiguration is applied to the flux limiter functions in MUSCL. Two reconfigurable partitions are created for Turbulence MUSCL and Convection MUSCL. All limiter functions are developed independently and synthesized separately from the top MUSCL module. Required limiter functions for both MUSCLs are loaded dynamically without interfering each other operation. This implementation has successfully reduced the resource utilization by 60%. Total power consumption is also reduced by 29%. Configuration speed is improved by 15-times faster as compared to fully reconfiguration method. All implemented functions achieved at least 17 times speed-up compared with the software implementation.