Agile Software development methodology is most emerging in software development, there has been a significant contribution from many researchers towards estimating the size, cost, schedule, effort and duration. However, the approaches reported in the literature lack in considering the evolution of biological systems for better optimization in agile. Here Agile Estimation Plan method determines the story size but the velocity is not properly defined and Harmony Search algorithm is adopted and modified in improvisation process towards agile to calculate the better velocity for each end of the iteration plan. This method help to improve the optimization while compare with normal agile process. The experimental results show how the harmony agile process is better than the normal agile process and it shows the efficiency of the method.