In this paper, a previously proposed method for story stiffness estimation of steel residential house is extended to estimate story stiffness of wooden residential houses considering non‐structural walls based on the available design information, that is, story weights, wall type, wall length, and wall opening type. Microtremor measurement data of several newly constructed buildings are used to determine unknown model parameters of stiffness estimation function, which minimize the estimation error of eigen frequency. The proposed method can simultaneously estimate the standard stiffness of wall element common to the same specification and the effects of wall opening and wall shape. The validity of the proposed method is examined by using measured actual microtremor records and drawing information of wall types and wall lengths of 19 wooden residential houses.