Machine learning predictions of molecular thermochemistry, such as formation enthalpy, have been limited for large and complicated species because of the lack of available training data. Such predictions would be important in the prediction of reaction thermodynamics and the construction of kinetic models. Herein, we introduce a graph-based deep learning approach that can separately learn the enthalpy contribution of each atom in its local environment with the effect of the overall molecular structure taken into account. Because this approach follows the additivity scheme of increment theory, it can be generalized to larger and more complicated species not present in the training data. By training the model on molecules with up to 11 heavy atoms, it can predict the formation enthalpy of testing molecules with up to 42 heavy atoms with a mean absolute error of 2 kcal/mol, which is less than half of the error of the conventional increment theory. We expect that this approach will also enable rapid prediction of other extensive properties of large molecules that are difficult to derive from experiments or ab initio calculation.