Hydrothermal growth takes place in a closed cylindrical container called an autoclave. Natural convection flow of an aqueous solution at a high temperature and a high pressure carries the nutrient. The high temperature growth condition and the natural convection flow are maintained by two independently controlled electrical heaters on the outside of the autoclave. In practice, the heating is circumferentially non-uniform. Many theoretical and numerical studies, however, assume axially symmetric heating conditions. This paper presents a numerical analysis of the three-dimensional heat transfer and fluid flow with a non-uniform heating condition. The analysis is based on an industry-size autoclave with an aspect ratio of 10. The non-uniform heating is introduced on the surface of the lower dissolving chamber and the upper growing chamber of an autoclave with or without a baffle at the middle height. The flow and temperature patterns are obtained. The circumferentially non-uniform surface temperature has dramatic effects on the fluid flow and therefore the temperature distribution in the bulk fluid. With a temperature deviation, the flow is three-dimensional. When only the dissolving chamber is subjected to circumferentially non-uniform heating, a baffle is essential to create a uniform growth environment in the growing chamber. Based on a parametric study, it is evident that in order to obtain high-quality single crystals wall temperature control on the growing chamber wall is more important than that on the dissolving chamber wall.