Subcritical hydrothermal liquefaction (HTL) has exhibited significant potential in the treatment of antibiotic fermentation residue (AR), but the synchronous recycling of the multiple nutrients in AR by HTL has not been considered previously. A comprehensive understanding of the transformation mechanism of nutrients is the prerequisite of their recycling. Results showed that 85.8–88.9% of phosphorus (P) was enriched in hydrochar by adsorption to Al/Fe (hydro)oxides or precipitation as Ca/Mg minerals, while most nitrogen (N) was released into the liquid phase due to the poor affinity between metal cations and nitrogen species. Moreover, the distribution and evolution of nutrients were controlled by temperature. Increasing temperature promoted the production of the recyclable NH4+–N and apatite-P. Above 220 °C, the increased apatite-P was mainly derived from the transformation of the unstable non-apatite inorganic-P. Further, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) analysis indicated that the dissolved organic-N with N3–4 as the prominent components (180–220 °C), especially proteins, were converted into NH4+–N and stable lignins/carboxyl-rich alicyclic molecule (CRAM)-like compounds via a series of depolymerization, deoxidation, deamination, and cyclization reactions as the temperature increased. Undoubtedly, this work will guide the directional regulation of the distribution and speciation of AR-derived nutrients, and have important implications for optimizing nutrients’ recycling and sustainable biowaste management.