A three-dimensional reconstruction method using shadowgraphy for complex shaped bubbly flows is proposed. Bubble distribution is represented by a metaball object. Metaballs have the capability of representing smooth but complex surfaces. The fundamental strategy is searching the optimal metaball object equivalent to the original bubble distribution. The method does not assume that every bubble has a certain size or shape, therefore, intensive image processing on shadow images is not required. This method has applied to both synthetic bubble shadow images and those obtained from a real experiment, and the results indicate the potential ability of bubble reconstruction.