One-dimensional photonic crystals composed of silicon and air layers with and without twinning defect (i.e., a periodicity break where one half of the photonic structure is a mirror image of the other one) are studied by means of terahertz time-domain transmission and reflection spectroscopy. The structure with defect is decomposed into building blocks: two twins and a defect. A phase-sensitive characterization in transmission and reflection allows us to fully determine the transfer matrices of any block and consequently to predict the properties of composed structures regardless of the microstructure of the constituting blocks. It is shown and experimentally demonstrated that the defect level position is controlled by the reflectance phase of the twins. Possible approach of the reflectance phase determination by use of Kramers-Kronig analysis is also discussed.