Purpose Postoperative complications are known to influence short-term mortality, however, their association with long-term mortality remains incompletely characterised. This study aimed to evaluate the association between postoperative complications and long-term all-cause mortality after gastrointestinal cancer surgery in Aotearoa New Zealand. Methodology A retrospective population-based cohort study was conducted of adults undergoing major gastrointestinal and hepatobiliary cancer resection in New Zealand public hospitals between 2005 and 2020. Postoperative complications within 90-days were classified using administrative coding. The primary outcome was all-cause mortality at 1, 3 and 5 years after surgery. Survival was analysed using Kaplan-Meier curves and Cox proportional hazards regression, with time-varying effects modelled across postoperative intervals, adjusted for patient-, disease-, and operative factors. Results The study included 31,199 patients with 14,646 (46.9%) experiencing at least one complication. Median follow up was 12.3 years. Patients with complications had significantly poorer long-term survival (p<0.001). On adjusted Cox regression analysis, complications were an independent predictor of mortality in the early postoperative period (0-1 month; HR 8.80, 95% CI 6.71-11.54), with a persistent effect at 1-3, 3-9, and 9-18 months. The association attenuated but remained significant from 18 months to 5 years (HR 1.26, 95% CI 1.19-1.34) and from 5 to 10 years (HR 1.25, 95% CI 1.15-1.36) but was not apparent beyond 10 years (HR 1.07, 95% CI 0.93-1.24). Conclusion Postoperative complications are independently associated with poorer long-term survival following gastrointestinal cancer resection, with strong early impacts but persisting for over 5 years after surgery. These findings highlight the importance of strategies targeting complication prevention and early management to improve long-term outcomes.