The approach for achieving efficient and clean combustion in a diesel–natural gas (NG) heavy-duty engine at low loads was studied by computational fluid dynamics simulation. This study proposed the concentration and temperature-stratified combustion technology and clarified its mechanism. The results revealed that different stratified combustions can be organized by controlling the pressures, timings, and durations of diesel and NG injections, and stratified combustion can be classified into moderate, lean, and rich stratified combustion modes. Efficient and clean combustion can be realized simultaneously at low engine loads: the gross indicated thermal efficiency (ITEg) of engine breakthrough was improved to 47.9%, and the indicated-specific emissions of unburned hydrocarbon (ISUHC) were greatly reduced to 1.6 g/kWh, while the indicated-specific emissions of nitrogen oxide (ISNOx) remained at 0.6 g/kWh. Moreover, the detailed analysis of three typical stratified combustion modes demonstrates that coupling control of the concentration and temperature of the charge is the key to obtaining excellent engine performance. Most of the NG-stratified mixture should burn in the react ratio range of 0.4 to 0.8 for low unburned hydrocarbon emissions, low nitrogen oxides emissions, and rapid combustion. The proper temperature stratification should ensure that a high-temperature charge is around the over-lean NG mixture. This study can provide the fundamentals of stratified combustion control and feasible solutions for commercial applications of NG engines.