This paper presents a comparative study on combustion and emissions of hydrogen-enriched biogas premixed charge direct injection dual-fuel (DIDF) engine and indirect injection dual-fuel (IDIDF) engine. The results show that the IDIDF engine outperforms the DIDF engine in terms of higher indicative engine cycle work (Wi) and lower emissions of CO, soot, and noise, but the disadvantage is higher NOx emission. Under the same fueling condition, the IDIDF engine’s Wi is on average 6% higher than that of the DIDF engine, but the NOx concentration in the combustion products of the IDIDF engine is 1.5 times higher than that of the DIDF engine. The IDIDF engine creates the stratified mixture distribution with higher O2 concentration in the auxiliary combustion chamber, which is favorable for auto-ignition and reduces the ignition delay. The biogas composition affects slightly CO and soot emissions, but significantly affects NOx emission. When the methane composition in biogas increases from 60% to 80%, the soot volume fraction is approximately 0.1 ppm in both types of combustion chambers, the CO concentration varies from 1.4% to 1.8%, and the NOx concentration varies from 3000 to 5000 ppm in the case of IDIDF engine and 2500–4500 ppm in the case of DIDF engine. For both types of dual-fuel engines, when engine speed increases, CO concentration and the soot volume fraction increase, while Wi and NOx concentration decrease.