Ammonia combustion does not produce carbon dioxide, and has been recognized as one of the promising approaches to achieving carbon neutrality in transportation sector. Due to the slow flame propagation speed and high ignition energy requirements, reactive fuel pilot ignition is essential for ammonia combustion in compression ignition engines. The reduction of pilot fuel drives CO₂ mitigation by curtailing carbon input, but this has a demand of advanced combustion modulation techniques to sustain engine efficiency. Designed pilot fuel stratification enables an activated in-cylinder environment, overcoming the difficulty in ammonia ignition and combustion, and allowing for a minimal pilot fuel amount to trigger premixed ammonia combustion. The minimum pilot fuel permits 99.1% ammonia energy substitution, accounting for only 1.3% of the CO₂ emissions from diesel combustion at the same load condition. Optimized intake organization coupled with improved reactivity stratification also achieves over 46% brake thermal efficiency, and reduces unburned ammonia by over 80% compared to baseline operation.