Since the start of the 21(superscript st) century, significant and unexpected non-traditional security threats have increasingly spread around the world, and have included natural disasters in northeastern Japan in 2011 and man-made disasters on September 11, 2001. Following the 911 incident, the government of the United States has actively established its homeland security system. Based on its practical experience and academic research, the focus has shifted from the early phase of counter-terrorism to the preparedness and resilience to disasters in the aftermath of Hurricane Katrina. A reform of the emergency management mechanism has been proposed, with particular emphasis being placed on organizational coordination and integration under the homeland security system. This paper analyzes the infrastructure of the U.S. homeland security system and the reform of the emergency management mechanism. The correlation between homeland security and its emergency response are also discussed along with the application in responding to non-traditional security threats.