McGaugh is the author of over 150 refereed publications that have been cited more than 16,000 times. He ranks in the top 2% of the top 2% of impactful authors across all sciences in the Stanford-Elsevier Updated science-wide author databases of standardized citation indicators and in the top 100 of those working in astronomy & astrophysics (of over 49,000 listed in that field in the top 2% database). He is thanked in the acknowledgements of over 200 papers of which he is not an author, and blogs about science at a high but accessible level.
McGaugh has made important contributions to multiple fields, including low surface brightness galaxies, galaxy dynamics, elemental abundances, stellar populations, cosmology, dark matter, and modified gravity. He demonstrated that low surface brightness galaxies are more common than had previously been thought, settling a decades-long debate over Freeman's Law. He and his collaborators discovered that low surface brightness galaxies are dark matter dominated, the central density relation, and the radial acceleration relation. He showed that baryonic mass (rather than luminosity) was the salient variable in the Tully-Fisher relation, coining the term "Baryonic Tully-Fisher relation." In addition to his observational work, McGaugh has had success as a theorist, correctly predicting the first-to-second peak amplitude ratio of the acoustic power spectrum of the cosmic microwave background, the rotation speeds and velocity dispersions of numerous dwarf galaxies including the dwarf satellites of Andromeda and the ultradiffuse Local Group object Crater 2, the outer slope of the rotation curve of the Milky Way early reionization, the redshift and amplitude of the 21 cm absorption signal at cosmic dawn, and the formation of massive galaxies at high redshift.