As a potential bioremediation strain for Pb contamination, Penicillium oxalicum SL2 sometimes has secondary activation of Pb, so it is crucial to clarify its effect on Pb morphology and its intracellular response to Pb stress. We investigated the effect of P. oxalicum SL2 in medium on Pb2+ and Pb availability in eight minerals, and revealed the prioritization of Pb products. (i)Pb was stabilized within 30 days as Pb3(PO4)2 or Pb5(PO4)3Cl with sufficient phosphorus (P); (ii) under P deficiency but sulfur (S) sufficient, Pb was stabilized mainly in the form of PbSO4; (iii) under conditions of P and S deficiency, Pb was stabilized mainly in the form of PbC2O2. With the help of proteomic and metabolomics analysis, a total of 578 different proteins and 194 different metabolites were found to be matched in 52 pathways. Among them, the activation of chitin synthesis, oxalate production, sulfur metabolism and transporters improved the Pb tolerance of P. oxalicum SL2, and promoted the synergistic effect of extracellular adsorption, bio-precipitation and transmembrane transport on Pb stabilization. Our results fill the gap in the intracellular response of P. oxalicum SL2 to Pb and provide new insights into the development of bioremediation agent and technology for Pb contamination.