To avoid colliding against, the high-speed railways are always constructed in double lines. In the operation of single-stopping pattern, the operators just need to dispatch trains in the safe headway. But in the pattern of multi-stops, the operation is rather complicated in the initial timetables. Traditionally, the initial tables are decided first in the process of timetabling and then the solving of conflicts are made to ensure the safety of operation. The initial timetables include the plans to run all trains stopping in different patterns. Because the operation is the pattern of multi-stops, the conflicts among trains are inevitable. The more complicated in the mixture of stopping pattern the more numbers of conflicts are. The issue will be a challenge to the operation of Taiwan High Speed Railway. To solve the problem, we constructed three simulation models to detect and solve the conflicts in the initial timetables. The approaches employed in the models were express preempting, safe separating and conditional waiting. Three models were also tested by the planning data of Taiwan High Speed Rail. The results showed that express preempting would result in much more waiting time to more-stop trains. Safe separating would reduce the effective capacity of line. Conditional waiting could get an eclectic result between both approaches cited above.