Abstract Background Youth mental health is a major global concern with substantial inequities for Indigenous and other young people from minoritised ethnic groups. In New Zealand, Māori, the Indigenous people, experience poorer mental health than other young people, especially those living in high deprivation. Cultural connectedness is related to positive mental wellbeing, however, its potential to buffer against the harms of structural disadvantage for young Māori mental health has not been investigated. Methods We used data from 1224 Māori young people in the longitudinal Growing Up in New Zealand study. Structural disadvantage measures included material hardship, deprivation, employment, residential mobility. We conducted Latent Class Analysis and Social Sequence Analysis to identify clusters and longitudinal patterns of structural disadvantage. Cultural connectedness and mental wellbeing (depression & anxiety symptoms, quality of life) were measured at age 12. Linear regression analysis was used to determine associations between structural disadvantage, cultural connectedness and mental health. Results We identified 3 trajectories of structural disadvantage for Māori youth: 21% experienced persistent high structural disadvantage, 35% intermittent high structural disadvantage and 44% persistent relatively low structural disadvantage. Few differences in mental health were found between groups. Cultural connectedness was independently associated with positive mental wellbeing, yet there was mixed evidence it might buffer the impacts of structural disadvantage on mental health. Conclusions Our results highlight the importance of policies that uphold Indigenous rights to health and address structural disadvantage as a persistent threat to Indigenous wellbeing. Our findings call for holistic, early-life, family-centred strategies and to reduce barriers to accessing support. We highlight the need for policies that enable young people to flourish in their identity and culture. Key messages • Many Māori young people experience pervasive structural disadvantage starting before they are born, persisting throughout childhood and adolescence which is an omnipresent threat to their wellbeing. • Supporting cultural connectedness for Indigenous youth is important but cannot substitute for policies addressing structural disadvantages that contribute to health inequities.