We estimate the displacement energy of Lagrangian 3-spheres in a symplectic 6-manifold $X$, by estimating the displacement energy of a one-parameter family $L_{lambda}$ of Lagrangian tori near the sphere. The proof establishes a new version of Lagrangian Floer theory with cylinder corrections, which is motivated by the change of open Gromov-Witten invariants under the conifold transition. We also make observations and computations on the classical Floer theory by using symplectic sum formula and Welschinger invariants.