We present modelling of line polarization to study multi-dimensional geometry of stripped-envelope core-collapse supernovae (SNe). We demonstrate that a purely axisymmetric, two-dimensional geometry cannot reproduce a loop in the Stokes Q-U diagram, i.e., a variation of the polarization angles along the velocities associated with the absorption lines. On the contrary, three-dimensional (3D) clumpy structures naturally reproduce the loop. The fact that the loop is commonly observed in stripped-envelope SNe suggests that SN ejecta generally have a 3D structure. We study the degree of line polarization as a function of the absorption depth for various 3D clumpy models with different clump sizes and covering factors. Comparison between the calculated and observed degree of line polarization indicates that a typical size of the clump is relatively large, >~ 25 % of the photospheric radius. Such large-scale clumps are similar to those observed in the SN remnant Cassiopeia A. Given the small size of the observed sample, the covering factor of the clumps is only weakly constrained (~ 5-80 %). The presence of large-scale clumpy structure suggests that the large-scale convection or standing accretion shock instability takes place at the onset of the explosion.