As in the title, I want some references about theories for elliptic curves over rings(not fields) or over schemes. I heard that behaviours(?) of such elliptic curves are not as simple as elliptic curves over fields. Could anyone suggest me any references(books, papers, lecture notes, etc)?
You could try reading (the relevant parts of) Qing Liu's book on Algebraic geometry or the book on Neron models by Bosch-Lutkebohmert-Raynaud to get a feeling for elliptic curves over one-dimensional schemes. You could also try reading some papers where abelian schemes are used, e.g., Szpiro's asterisque (1985) on the Mordell conjecture, or Jinbi Jin's paper http://arxiv.org/abs/1303.4327 on equations for the modular curve $Y_1(n)$ over $\mathbf Z[1/n]$.