Diesel/natural gas dual fuel engine is acquiring more and more attention due to its potential to reduce NOX and soot emission simultaneously. Micro-pilot-induced diesel ignition natural gas engine is a popular manner to further improve the emission reduction capability of dual fuel engine. A six cylinder, four stroke, commonrail diesel engine is converted into dual fuel engine. Natural gas is injected into the intake manifold after the throttle. Five gas injection valves are used to control natural gas flow rate. Based to the established fuel supply system, a dual fuel control system is developed by using MS9S12XEP100 MCU. Voltage boosting circuit, fuel injector driving circuit, gas injection valve driving circuit and MeUn driving circuit are integrated on the platform of MCU hardware. Two ECU is connected to each other by CAN bus and several I/O ports to fulfil the fuel injection functional requirement. A software framework involves gas injection timing synchronization, fuel mode managing, multi-time injection. A MAP based fresh air mass flow rate and intake charge efficiency model is integrated in the MCU to calculate the fresh air quality in cylinder. The last part is performance optimization research at low load. Ignition diesel is divided into two stages, and the first injection timing, first injection ratio and injection pressure are used as controllable parameter to reduce NOX and HC emission. Experimental result reveal that by dividing ignition injection into two stage and advancing first injection to 60°CA BTDC CH4 emission can be reduced by 77% while NOX remains unchanged. Increasing the first injection ratio and injection pressure can also reduce THC emission. If injection pressure is higher than 75MPa, the effect of HC reduction effect is not that obvious. Experimental results shows that developed control system can accomplish the functional requirements of dual fuel engine management. Emission test results demonstrate that IMO TierII can be satisfied at diesel mode. DF mode emission performance can meet the requirement of IMO TierIII. Furthermore, as the first domestic product dual fuel dedicated control system, which has passed through the CCS authentication in China, the engine emission level can meet the current and upcoming China’s emission standard on non-road engine on the premise of guaranteeing engine power and economy.