The transition between free flow and congestions in traffic can be observed in our daily life. Although this traffic phenomenon is well studied in highways, traffic in a network scale (representing a city) is far from being understood. A fundamental unsolved question is how the global flow in a city is being integrated from local flows. Here, we identify a fundamental mechanism of traffic organization in a network scale as a percolation process, and we show how global traffic breaks down when identified bottlenecks are congested. These bottlenecks evolve with time according to traffic dynamics and are different from structural bottleneck links found by traditional network analysis. Improvement of traffic on these bottlenecks can significantly improve the global traffic.