SHP-1, as a protein tyrosine phosphatase, plays a key role in inflammation-related diseases. However, its function and regulatory mechanism in the imbalance of inflammatory response and acute liver injury during sepsis are still unknown. Herein, we constructed a murine model of Escherichia coli (E. coli) sepsis and demonstrated the function and novel mechanism of SHP-1 in sepsis. Overexpression of SHP-1 significantly reduced the mortality rate of mice and alleviated the histopathological deterioration of liver. In addition, it inhibited the expression and release of pro-inflammatory mediators in liver tissue and serum, but upregulated the expression of anti-inflammatory molecules. Silencing SHP-1 exhibited the completely opposite effects. Furthermore, the transcriptome data of mice liver showed that SHP-1 suppressed the progression of sepsis by negatively regulating the activation of multiple inflammation-related signaling pathways. More importantly, we fully revealed the regulation mechanism of SHP-1 on both canonical and non-canonical nuclear factor kappa-B (NFκB) signaling pathways during sepsis for the first time. SHP-1 significantly inhibited the phosphorylation and nuclear translocation of p50, while p65 inhibition was mainly achieved by inhibiting its transcription and translation levels. Meanwhile, SHP-1 inhibited the phosphorylation and nuclear translocation of p52, thereby inhibiting the activation of non-canonical NFκB signaling pathways. In summary, SHP-1 negatively regulated canonical and non-canonical NFκB signaling pathways, thereby blocking the occurrence of excessive inflammatory response and acute liver injury caused by E. coli sepsis. Our findings systematically elucidate the role and mechanism of SHP-1 during sepsis, providing new insights into the prevention and treatment of inflammation and immune-related diseases.