We studied a low-field giant magnetostrictive spin-flop transition in a colossal magnetoresistance manganite La1.4Sr1.6Mn2O7 using resonant soft x-ray diffraction and soft x-ray absorption spectroscopy at the Mn L2,3 edge. The spin-flop transition is induced by an instability of magnetocrystalline anisotropy near a critical eg orbital configuration with a balanced occupation in dx2−y2 and d3z2−r2 states, which contribute in-plane and out-of-plane orbital angular momenta, respectively. The magnetic field drives a certain change in the orbital occupation with lattice distortion to switch the magnetic anisotropy, resulting in the spin-flop transition. These results provide a comprehensive mechanism of interplay between spin, orbital, and lattice degrees of freedom to realize a low-field giant magnetoelasticity.