Protein therapy, an innovative therapeutic strategy, has been extensively used in the treatment of cancer in recent years. However, the sequential delivery of multiple proteins acting separately intracellular and extracellular to their sites of action remains a challenge. Here, we construct a nanosystem (PEI-PEG-TRAIL@IONP-GOx) to sequentially release tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) extracellularly and glucose oxidase (GOx) intracellularly for synergistic cancer treatment. The nanosystem is built as a core-shell structure. The core is a pH responsive nanoassembly of boronic acid modified iron oxide nanoparticles (FPBA-IONPs) and polyphenol decorated GOx. The shell is a PEGylated polyethyleneimine (PEI-PEG) polymer on which TRAIL was coupled by a matrix metalloproteinase-2 (MMP-2) responsive peptide. Once the nanosystems were magnetically guided to the tumor site, TRAIL was quickly released by the extracellular MMP-2 to induce tumor apoptosis and enhanced the cellular uptake of the cores. After cytosolic delivery, FPBA-IONPs and GOx were disassembled intracellularly to trigger a cascade reaction to generate free radicals for tumor inhibition. Both in vitro and in vivo experiments proved the separate delivery of TRAIL and GOx and their remarkable synergistic anti-cancer effect. We believe that this nanosystem can offer a new approach for the multistage delivery of proteins and accomplish the objective of protein cooperation for cancer treatment.