The primary mechanism for organisms to react to their rapidly changing environments is by alteration of gene expression profiles. An organism is capable of doing so, via small molecules that integrate extracellular cues and relay them intracellularly through cognate receptor binding. Hence small molecules act as principle mediators of organismal development and studying their regulation and interactions with other biomolecules including DNA and coregulatory proteins can provide critical insights into organismal physiology. The work presented in this dissertation combines liquid-chromatography – mass spectroscopy (LC-MS) based metabolomics with protein biochemical studies to explore the small molecule – receptor biology in the nematode C. elegans. In C. elegans, steroidal small molecule ligands called dafachronic acids (DAs) regulate reproductive development and lifespan through interaction with the conserved nuclear receptor DAF-12. While some of the key enzymes in DA biosynthesis pathway are well studied, many aspects of DA receptor interactions, their biosynthesis and metabolism remain to be uncovered. In the first part, we characterize DAF-40 as the critical DA-oxidoreductase that uses known DAs as precursors in the biosynthesis of highly unstable, yet highly potent DAF-12 ligands to mediate reproductive development. It uncovers the complex pool of chemically labile DAF-12 ligands and adds a novel steroid metabolome regulatory node. Next, we investigate the intersection of DA/DAF-12 signaling with DAF-12 receptor homologs - NHR-8 and NHR-48. We complement protein biochemistry studies with metabolomics and reveal the dimeric interactions between these receptors and correspondingly their role in coregulating the lipid metabolome. Lastly, while the pivotal roles of the DA family of steroids have been acknowledged, a systematic exploration of the structural and hence functional diversity of steroids has not been achieved in C. elegans or any other animal model system. In the final chapter, we implement a 13C stable isotope-based metabolomics approach that uncovers the striking structural diversity in steroidal small molecules. We reason the use of these novel steroids as a starting point to mine for other nuclear receptor ligands in nematodes. As a whole, this dissertation delves into the deeply interconnected steroid and lipid metabolism network that controls nematode physiology via nuclear receptor interactions. With the findings presented here, we aim to complement the extensive genomics and proteomics in nematodes with a comprehensive structural and functional characterization of the metabolome.