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Unfavorable ecosystems in Bangladesh are under intense pressure of crop production and climate change impact; although the relationships of indigenous soil nutrients ratios with crop performance are yet to be fully explored. Experiments were conducted under submergence and cold prone areas (agricultural ecological zone, AEZ-3), drought and cold prone areas (AEZ-26), non-saline tidal flood ecosystem (AEZ-13), char and saline prone ecosystem (AEZ-18) and haor ecosystem (AEZ-21) for evaluating rice grain yield with native nutrients ratios. Synergistic and antagonistic relationships were observed in different AEZ depending on indigenous nutrient ratios. The Ca:P and N:Zn ratios were playing significant negative role with rice yield in wet season. In dry season, P:K ratio was acting antagonistically in AEZ-18, AEZ-3 and AEZ-26 but K:Mg, Ca:Zn S:Zn P:Zn were playing synergistic role in the same localities. The C:K ratio was playing antagonistic role with dry season irrigated rice yield in AEZ-13 and AEZ-21. Dry season irrigated rice grain yield was 13-27% lower in AEZ-26 than others AEZ because of variations in negative ratios of nutrients. Application of 187-13-75-15-1.1, 174-27-19-840, 162-11-58-11-0, 180-24-14-15-4 and 144-36-5-3-0 kg/ha of N-P-K-S-Zn, respectively for Rangpur, Rajshahi, Barisal, Sonagazi and Habiganj improved dry season rice yield significantly in all AEZ except AEZ-18 compared to indigenous soil fertility. Soil separates showed variable relationships with indigenous nutrient ratios in different AEZ. It is concluded that indigenous soil nutrient ratios play a vital role in improving rice yield under unfavorable ecosystems.