Limiting nitrogen supply has been routinely used as the master regulator to direct lipid biosynthesis. However, this strategy does not work with nitrogen-rich substrates, such as Jerusalem artichoke (JA), a fructose-based biomass, while it is difficult to obtain a high carbon-to-nitrogen (C/N) molar ratio. In this study, an alternative strategy to promote lipid accumulation by the oleaginous yeast Trichosporon fermentans CICC 1368 was developed by limiting phosphorous supply, and this strategy was implemented with JA hydrolysate as substrate. We showed that lipid accumulation was directly correlated with the C/P ratio of the culture media for T. fermentans. The time course of cell growth and lipid production was analyzed in a media with an initial C/P ratio of 6342, and the cellular lipid content could reach up to 48.5% of dry biomass. Moreover, JA hydrolysates were used as substrate for microbial lipid accumulation, under high C/P molar ratio condition, lipid yield, lipid content, and lipid coefficient increased by 10, 30, and 34%, respectively. It showed that by limiting phosphorus, the conversion of sugar into lipids can be improved effectively. Limiting phosphorus provides a promising solution to the problem of microbial lipid production with nitrogen-rich natural materials.