Combined heat and power systems (CHPs) have received much attention in recent years due to increasing use of bio-fuels and distributed generation (DG). Conventionally, they are connected to the power grid to balance electrical demands and supplies. This research investigated an off-grid (stand-alone) biofuel micro CHP system with hybrid energy storage (HES) (including battery banks and super-capacitors) by developing an energy management strategy based on dynamic programming (DP). DP is an optimization strategy which has been applied to energy systems in recent years. However, they suffer from dimension problems when the number of variables increases. This work is the first attempt to apply the decision tree (DT) to multi-dimension DP solutions in energy systems. The energy efficiency is improved from 45.77% to 57.97% using diesel-biofuels and the system has a potential for commercial applications. The experimental test results validate its feasibility and effectiveness.