One of the most extensively studied questions in oleaginous microorganism is how cells alter gene expression to deal with growth-limiting perturbation, and resource allocation was especially recognized to contribute to TAGs accumulation. However, the strategies of resource allocation are poorly understood. Here, we examined how metabolic alternations induced by nitrogen starvation drive the TAGs accumulation in M. alpina by time-course phenotypes, metabolomics, lipidomics, and proteomic analyses.Our study offers a panoramic view of resource allocation of M. alpina in response to nutrient stress and reports a set of intriguing relations between resource reallocation and TAGs accumulation. This system-level insight provides a rich resource to explore in-depth functional characterization and informs a nutrient stress manipulation strategy of combining strain development and process integration to achieve better lipid productivity.