This review discusses the importance of fusion protein linkers in the construction of stable and bioactive recombinant fusion proteins. Linkers, which connect functional domains, play a crucial role in improving the properties of fusion proteins. The review covers the general properties of linkers derived from naturally-occurring multi-domain proteins, which serve as a foundation for empirical linker design. Empirical linkers are categorized into three types: flexible, rigid, and *in vivo* cleavable linkers. Flexible linkers, rich in small or polar amino acids, provide flexibility and allow for interdomain interactions. Rigid linkers, such as α-helical or Pro-rich sequences, maintain a fixed distance between domains. *In vivo* cleavable linkers, designed to be cleaved under specific conditions, release free functional domains, improving bioactivity and targeting. The review also highlights the use of linker designing tools and databases to aid in the rational design of linkers. Additionally, it discusses the various functions of linkers, including improving folding and stability, enhancing expression yield, increasing biological activity, and achieving desirable pharmacokinetic profiles.This review discusses the importance of fusion protein linkers in the construction of stable and bioactive recombinant fusion proteins. Linkers, which connect functional domains, play a crucial role in improving the properties of fusion proteins. The review covers the general properties of linkers derived from naturally-occurring multi-domain proteins, which serve as a foundation for empirical linker design. Empirical linkers are categorized into three types: flexible, rigid, and *in vivo* cleavable linkers. Flexible linkers, rich in small or polar amino acids, provide flexibility and allow for interdomain interactions. Rigid linkers, such as α-helical or Pro-rich sequences, maintain a fixed distance between domains. *In vivo* cleavable linkers, designed to be cleaved under specific conditions, release free functional domains, improving bioactivity and targeting. The review also highlights the use of linker designing tools and databases to aid in the rational design of linkers. Additionally, it discusses the various functions of linkers, including improving folding and stability, enhancing expression yield, increasing biological activity, and achieving desirable pharmacokinetic profiles.