MYCNamplification is an independent risk factor for poor prognosis in neuroblastoma (NB), but its protein product cannot be directly targeted due to protein structure. Thus, this study aimed to explore novel ways to indirectly target N-Myc by regulating its posttranslational modifications (PTMs) and therefore protein stability. N-Myc co-immunoprecipitation combined with HPLC–MS/MS identified 16 PTM residues and 114 potential N-Myc interacting proteins. Notably, both acetylation and ubiquitination were identified on lysine 199 of N-Myc. We then discovered that p300, which can interact with N-Myc, modulated the protein stability of N-Myc in MYCN-amplified NB cell lines, and simultaneously regulated the acetylation level on lysine-199 and ubiquitination level of N-Myc protein in vitro. Furthermore, p300 correlated with poor prognosis in public NB datasets. Taken together, p300 can be considered as a potential therapeutic target to treat MYCN-amplified NB patients, and other identified PTMs and interacting proteins also provide potential targets for further study.