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Previously, the Taiwan Light Source (TLS) has proven the good beam quality mainly depends on the utility system stability. A series of efforts were devoted to these studies. Further, a high precision temperature control of the RF de-ionized cooling water system has been achieved to meet the more critical stability requirement. The paper investigates the mixing mechanism through thermal and flow analysis and verifies the practical influences. A flow mixing mechanism and control philosophy is studied and processed to minimize temperature variation which has been reduced from ± 0.1 °C to ± 0.01 °. Also, the improvement of correlation between RF performance and water cooling stability is presented.