The coexistence and coupling of ferroelasticity and magnetic ordering in a single material offers a great opportunity to realize novel devices with multiple tuning knobs. Complex oxides are a particularly promising class of materials to find multiferroic interactions due to their rich phase diagrams, and are sensitive to external perturbations. Still, there are very few examples of these systems. Here, we report the observation of twin domains in ferroelastic LaCoO3 epitaxial films and their geometric control of structural symmetry intimately linked to the material’s electronic and magnetic states. A unidirectional structural modulation is achieved by selective choice of substrates having twofold rotational symmetry. This modulation perturbs the crystal field–splitting energy, leading to unexpected in-plane anisotropy of orbital configuration and magnetization. These findings demonstrate the use of structural modulation to control multiferroic interactions and may enable a great potential for stimulation of exotic phenomena through artificial domain engineering.