Biodegradable polymer using inexpensive renewable resources such as starch produced poor mechanical, barrier properties and transparency of product, these properties were the important parameter for packaging material. This research intended to study the effect of glycerol monostearate (GMS) treated organo layer silicate (OLS) in biodegradable polymer starch masterbatch to eliminate the inferior properties. Focus was in morphological structure of biodegradable polymer starch clay nanocomposite. Biodegradable polymer starch clay nanocomposite was prepared using Haake Rheomix Polydrive at a temperature of 100 oC for 5 minutes and screw speed 60 rpm and the product was used as masterbatch to get a better dispersion of OLS in the matrix. Masterbatch was formulated with the parameter of 35%, 45% and 50% starch and 3.5% of OLS. Morphological structure of biodegradable polymer starch clay nanocomposite was characterized using Scanning Electron Microscope (SEM), Atomic Force Microscope (AFM) and X-Ray Diffraction (XRD) to observe the dispersion and compatibility of the organo layer silicate in biodegradable nanocomposite matrix. XRD analysis provided the dispersion of organo layer silicate at 35% starch was better than 45% starch and 50% starch in materbatch. This was consistent with the SEM and AFM result, masterbatch containing 50% starch had interfere the OLS dispersion and produced agglomeration of organo layer silicate. SEM images of masterbatch with 50% loading level of starch shown structure that starch not completely thermoplasticized.