The synthesis of biodiesel has been widely studied. There are many raw materials used for the synthesis either from edible or non-edible oil. In this study, we investigated the synthesis of biodiesel using two steps process. The synthesis at 60 oC and ozonation are running in consecutive ways. The waste cooking oil was prepared for synthesis at 60 oC for one hour. The mol ratio of waste cooking oil and methanol was 1:5 and 1.5 % w/w NaOH was used as catalyst. Sample from both synthesis at 60 oC and ozonation process have been analyzed using Gas Chromatography. It has been proved that transesterification product from synthesis at 60oC contained of long chain methyl esters, hence the reaction is esterification from long chain fatty acids to long chain methyl esters which consisted of saturated and unsaturated methyl esters. The dominants long chain methyl esters from synthesis at 60 oC were methyl palmitate, methyl oleat, methyl stearate. There were three unsaturated methyl esters produced which are methyl palmitoleate, methyl oleat and methyl linoleate. All these products were then ozonised at various temperatures. Short chain methyl esters which were from cracking of unsaturated methyl esters and long chain methyl esters remained as product. The short chain methyl esters are methyl nonanoate, methyl hexanoate, and methyl octanoate. Methyl nonanoate was a product from cracking of methyl oleate, whereas methyl hexanoate was a product of cracking of methyl linoleate .It was found that the best temperature used for ozonation was 20 oC.