Resource-constrained environments, such as embedded devices, have limited amounts of memory and storage. Practical programming languages such as C++ and Rust tend to output multiple similar functions by monomorphizing polymorphic functions. An optimization technique called Function Merging, which merges similar functions into a single function, has been studied. However, in the state-of-the-art approach, the number of functions that can be merged at once is limited to two; thus, efficiently merging three or more functions, which are often generated from polymorphic functions, has been impossible. In this study, we propose Multiple Function Merging optimization, which targets merging three or more similar functions into a single function using a multiple sequence alignment algorithm. With multiple aligned information, Multiple Function Merging can increase merge opportunities and reduce extra branching overheads at the code generation stage. We evaluated it using the SPEC CPU benchmark suite and some large-scale C/C++ programs, and the results show that it reduces code size by as much as 7.61% compared with the state-of-the-art approach.