Through our four years experiments on students' Scrum based agile software development (ASD) process, we have gained deep understanding into the human factors of agile methodology. We designed an agile project management tool - the HASE collaboration development platform to support more than 400 students self-organized into 80 teams to practice ASD. In this thesis, Based on our experiments, simulations and analysis, we contributed a series of solutions and insights in this researches, including 1) a Goal Net based method to enhance goal and requirement management for ASD process, 2) a novel Simple Multi-Agent Real-Time (SMART) approach to enhance intelligent task allocation for ASD process, 3) a Fuzzy Cognitive Maps (FCMs) based method to enhance emotion and morale management for ASD process, 4) the first large scale in-depth empirical insights on human factors in ASD process which have not yet been well studied by existing research, and 5) the first to identify ASD process as a human-computation system that exploit human efforts to perform tasks that computers are not good at solving. On the other hand, computers can assist human decision making in the ASD process.