The tunneling phenomena of cold atoms in double-well with different interaction (U) and tunnel coupling (J) were studied. Experiments cannot be interpreted completely by a two-site Bose-Hubbard model. Thus, a new model was introduced, in which the ground state and the first excited state of the double-well were used as state bases. The expression of Hamiltonian was derived under the new model, which explains the reason why the parameter isnot consistent with the experiment from a two-site Bose-Hubbard model. Furthermore, we figured out the fluctuation of entanglement degree of the atoms in the double-well, and directly described the whole process of tunneling with the population of particles in the three states.