Abstract： Based on theory of collaterals disease， it is considered that chronic atrophic gastritis(CAG) is a collaterals disease. The authors identify the microscopic pathological changes of CAG from theory of collaterals disease，and put forward two hypotheses： the pathogenesis evolution process of CAG is from collateral qi constraint(deficiency) and stagnation to phlegm stasis obstruct the collaterals(or dampness toxin stagnate the collaterals) and to accumulation of collateral obstruction， as well as the basic pathological link of stasis of minute collateral. Combined with macroscopic syndrome differentiation，the authors put forward three clinical experience thoughts，namely first differentiate Dredging collaterals and dispersing knots， then differentiate warm or cool； the treatment of qi and collaterals runs through the whole process； harmonization treatment method goes first and combined with mutual reference of microcosmic and macroscopic syndrome differentiation. The three thoughts aim to to guide the application of prescription and drug in clinic.