Pyrolysis-gas chromatographic mass spectrometry (Py-GC/MS) was used to determine the yield and chemical composition of the pyrolysis products of Schizochytrium limacinum. The pyrolysis was carried out by varying the temperature from 300 °C to 800 °C. It was found that the main decomposition temperature of Schizochytrium limacinum was 428.16 °C, at which up to 66.5% of the mass was lost. A further 18.7% mass loss then occurred in a relatively slow pace until 760.2 °C due to complete decomposition of the ash content of Schizochytrium limacinum. The pyrolysis of Schizochytrium limacinum at 700 °C produced the maximum yield (67.7%) of pyrolysis products compared to 61.2% at 400 °C. While pollutants released at 700 °C (12.3%) was much higher than that of 400 °C (2.1%). Higher temperature will lead to more pollutant (nitrogen compounds and PAHs) release,which is harmful to the environment. Considering the reasonably high yield and minimum release of pollutants, a lower pyrolysis temperature (400 °C) was found to be optimum for producing biofuel from Schizochytrium limacinum.