Recent years have witnessed a surge of approaches to use neural networks to help tackle combinatorial optimization problems, including graph optimization problems. However, theoretical understanding of such approaches remains limited. In this paper, we consider the geometric setting, where graphs are induced by points in a fixed dimensional Euclidean space. We show that several graph optimization problems can be approximated by an algorithm that is polynomial in graph size n via a framework we propose, call the Baker-paradigm. More importantly, a key advantage of the Baker-paradigm is that it decomposes the input problem into (at most linear number of) small sub-problems of fixed sizes (independent of the size of the input). For the family of such fixed-size sub-problems, we can now design neural networks with universal approximation guarantees to solve them. This leads to a mixed algorithmic-ML framework, which we call NN-Baker that has the capacity to approximately solve a family of graph optimization problems (e.g, maximum independent set and minimum vertex cover) in time linear to input graph size, and only polynomial to approximation parameter. We instantiate our NN-Baker by a CNN version and GNN version, and demonstrate the effectiveness and efficiency of our approach via a range of experiments.