Study of separation zone is so important in right-angled three-branch or four-branch open channel junctions. Some effective parameters in this case are inlet discharge ratio and flow depth which in this research the effect of inlet discharge ratio and weir height ratios (flow depth) on flow pattern and dimensions of separation zone has been simulated numerically. Investigation of numerical results showed that k-ω model well validated with experimental results and had good agreement, so that simulation error was less than 20%. Dimensions of separation zone in main and side channels were directly proportional with the inlet discharge ratio. Also as increases of height ratio of outlet weirs, flow depth increases and separation zone dimensions decreased. According to the analysis of numerical results, dimensions of separation zone in vertical direction, of the channel bed to water surface increased, so that for discharge ratio 0.6 and height ratio of outlet weirs 0.377, length of separation zone at the channel bed, 0.1 m up the bed and water surface was about 60 cm, 75 cm and 85 cm, respectively. So of the water surface towards the channel bed, length of separation zone decreased about %29.