Traffic congestion and traffic accident have been a serious and significant problem in Phnom Penh city because the population has increased every year. An insufficient traffic signal, non-standard geometry, driver behavior, and lack of traffic discipline are the main factors that affect traffic flow. Kdan Pir is a very important intersection that has connected between Khan 7 Makara and Khan Toul Kork. Many people are crossing this intersection. This is the reason that makes Kdan Pir intersection always has traffic congestion. This study analyzed the traffic flow at Khan Pir Intersection. The traffic flow was analyzed in a micro-simulation environment using traffic data obtained from the traffic count survey, between 7:00 and 20:00, on 04 November, 2019. With the new geometry of Kdan Pir Intersection, we proposed five alternative solutions for the traffic signalization system. Queue lengths and Level of Services (LOS) were used as indicators for the alternative comparison. Results showed that the best alternative is option five that has a good queue length and level of service.