Holographic interferometric tomography can provide reconstruction of instantaneous three-dimensional gross flow fields. The technique however confronts ill-posed reconstruction problems in practical applications. Experimental data are usually limited in projection and angular scanning when a field is captured instantaneously or under the obstruction of test models and test section enclosures. An algorithm, based on a series expansion method, has been developed to improve the reconstruction under the ill-posed conditions. A three-dimensional natural convection flow around two interacting isothermal cubes is experimentally investigated. The flow can provide a challenging reconstruction problem and lend itself to accurate numerical solution for comparison. The refractive index fields at two horizontal sections of the thermal plume with and without an opaque object are reconstructed at a limited view angle of 80$circ$. The experimental reconstructions are then compared with those from numerical calculation and thermocouple thermometry. It confirms that the technique is applicable to reconstruction of reasonably complex, three-dimensional flow fields.