The precise atomic positions and occupancies in (Ba,Ca)TiO₃ ceramics have been characterized by high angle annular dark field (HADDF)-scanning transmission electron microscopy (STEM), electron energy loss spectroscopy (EELS), and annular bright field (ABF)-STEM. EELS precisely determines the distribution of Ba, Ca, and Ti ions in the perovskite structure, confirming the occupancy of ∼7% Ca content at B-site in (Ba_0.75Ca_0.25)TiO₃, which is the first direct evidence of Ca occupancy at the B-site in (Ba,Ca)TiO₃ ceramics. ABF-STEM mapped the displacement of Ti ions and oxygen ions with respect to the center of Ba ions. By averaging the displacements of Ti and O ions in multiple single domains, it confirms the average Ti displacement of 0.263 Å, and large apical and equatorial oxygen displacement of 0.264 Å and 0.347 Å, respectively. Such great displacements in (Ba,Ca)TiO₃ compared to BaTiO₃ are direct evidence for the structure origin of the ferroelectric enhancement in Ca substituted BaTiO₃.