There are a large number of valuable substances in diatoms, such as neutral lipid and pigments. However, due to the lack of clear metabolic pathways, their applications are still limited. Recently, chemical modulators are found to be powerful tools to investigate the metabolic pathways of neutral lipids. Thus, in this study, to identify new neutral lipid accumulation effectors, we screened the natural products that we separated before in the model diatom Phaeodactylum tricornutum (P. tricornutum) by using Nile-red staining method. Two compounds, penicillide and verrucarin J which were isolated from two marine fungal strains, were identified to promote neutral lipid accumulation. However, penicillide and verrucarin J were also found to significantly inhibit the growth of P. tricornutum through specifically inhibiting the photosynthesis of P. tricornutum. Quantitative analysis results showed that penicillide and verrucarin J significantly increased total lipid and triacylglycerol (TAG) contents, which are consistent with previous Nile-red staining results. The expression of key genes such as DGAT2D, GPAT2, LPAT2, and PAP involved in TAG synthesis and unsaturated fatty acids also increased after penicillide and verrucarin J treatments. Besides, many TAG-rich plastoglobuli formed in plastids shown by increased lipid droplets in the cytosol. Finally, penicillide and verrucarin J were found to reduce the expression of synthetic genes of fucoxanthin, and consequently reduced the content of fucoxanthin, indicating that there might be crosstalk between lipid metabolism and fucoxanthin metabolism. Thus, our work exhibits two useful compounds that could be used to further study the metabolic pathways of neutral lipid and fucoxanthin, which will fulfill the promise of diatoms as low cost, high value, sustainable feedstock for high-value products such as neutral lipid and pigments.