A method and apparatus for processing reconstructed video using in-loop filter in a video coding system are disclosed. The method uses chroma in-loop filter indication to indicate whether chroma components are processed by in-loop filter when the luma in-loop filter indication indicates that in-loop filter processing is applied to the luma component. An additional flag may be used to indicate whether the in-loop filter processing is applied to an entire picture using same in-loop filter information or each block of the picture using individual in-loop filter information. Various embodiments according to the present invention to increase efficiency are disclosed, wherein various aspects of in-loop filter information are taken into consideration for efficient coding such as the property of quadtree-based partition, boundary conditions of a block, in-loop filter information sharing between luma and chroma components, indexing to a set of in-loop filter information, and prediction of in-loop filter information.