Objective To investigate the value of combining Helicobacter pylori (HP) virulence factor typing with pepsinogen (PG) in assessing HP infection-related gastric mucosal injury in children. Methods A cross-sectional study enrolled children presenting with gastrointestinal symptoms at Wuxi Children's Hospital from August 2023 to December 2024. Based on gastroscopic pathology, participants were assigned to a mild injury group (n=66) or a moderate/severe injury group (n=51). Serum PG levels and HP virulence factor typing (type I/II) were examined to evaluate the diagnostic performance of combined testing for mucosal injury severity. Results The moderate/severe injury group had higher serum PGI and PGII levels than the mild injury group (P<0.05), and type I HP infection predominated (85.7%). Receiver operating characteristic curve analysis showed the following diagnostic performance for moderate/severe gastric mucosal injury: type I HP plus PGI positivity yielded an area under the curve (AUC) of 0.781, specificity 62.1%, and sensitivity 82.4%; type I HP plus PGII positivity yielded an AUC of 0.742, specificity 90.9%, and sensitivity 47.1%; simultaneous positivity for type I HP, PGI, and PGII yielded an AUC of 0.775, specificity 60.6%, and sensitivity 82.4%. Conclusions Serum PG levels and type I HP infection are closely associated with gastric mucosal injury severity. Their combined detection demonstrates good diagnostic performance for grading injury severity and provides a noninvasive strategy for clinical assessment of HP-related gastric mucosal damage in children.