An investigation into the lips-guided-flow combustion chamber (LGFC) and Miller cycle was conducted on a highly intensified diesel engine under rated power conditions to improve thermal efficiency. The radius and depth of the chamber bowl and lips were optimized to intensify the guided flow and fuel/air mixing. The experimental and simulated results show that the LGFC had a higher fuel/air mixture quality and quicker combustion rate, leading to a higher indicated power and higher thermal efficiency. A late intake valve closing (LIVC) Miller cycle with a higher expansion ratio of 11 and a lower compression ratio of 8.2 was used to control the energy distribution of the thermodynamic cycle and reduce the mechanical and thermal loads. The results show that the maximum combustion temperature was decreased by about 45 K and the thermal efficiency was improved by 2.1%. The research results are useful to guide the improvement in thermal efficiency through combustion chamber design and Miller cycle application for highly intensified diesel engines.