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Convenient and consistent phase convention is important in the construction of the hadronic Lagrangian. However, the importance of phase convention has been overlooked for a long time, and the sources of different conventions are never explicitly addressed. This obscure situation can cause mistakes and misinterpretations in hadron physics. In this paper, we systematically analyze and compare the flavor <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>S</mi><msub><mi>U</mi><mn>3</mn></msub></mrow></semantics></math></inline-formula> phase conventions from the perspective of the quark model. All sources that could lead to different conventions are pointed out and carefully studied. With the tool of the quark model, we also clarify some misconceptions and demonstrate a consistent way to incorporate different conventions.