In recent years, swarm intelligence optimization algorithm is a research hotspot in the area of computational intelligence and artificial intelligence. And its application has already penetrated into many fields. In many kinds of intelligent algorithms, the firefly algorithm (FA) is a relatively novel algorithm and shows excellent performance. In this chapter, we introduced FA algorithm and its applications. First, we described the basic concepts of the FA algorithm. Then, we improved the FA by combining the characteristics of specific problems to solve various problems such as numerical optimization, clustering analysis and protein complexes discovering on protein-protein interaction network. We gave the detailed implement steps and the comparing results to show the feasibility of FA and extensive of its applications.