Graphene and graphene oxide (GO) films have been explored to develop an efficient laser desorption/ionization mass spectrometry (LDI-MS) platform for the analysis of chemically and biologically important small molecules. The GO films were prepared by layer-by-layer (LBL) assembly cycles (one to ten layers) with precisely controlled thickness and surface roughness which are important structural factors for laser energy absorption capacity and laser energy transfer for efficient LDI-MS analysis. Amino acids, saccharides, and pyrenylated molecules were analyzed by LDI-MS on the LBL assembled GO films to reveal their structural influence on LDI-MS analysis of small molecules. Then, the structural influence of LBL assembled GO films on synergistic effect was investigated to develop an efficient and widely applicable LDI-MS analysis platform with an additional multiwalled carbon nanotube (MWCNT) layer. We found that the optimum number of GO film layers for LDI-MS analysis was dependent on the chemical structures of small molecules, and the laser energy threshold needed for LDI of small molecules on GO/MWCNT films could be lowered as the number of LBL assembled GO films increased underneath the MWCNT layer.