In this present work, numerical analyses have been carried out regarding the effect of fuel supply and combustion efficiency upon co-flow and cross-flow micro-combustor. Initially, a numerical model of 16 mm length, 1 mm channel height and 0.2 mm thick wall were established for a non-premixed hydrogen-air co-flow micro-combustor. Now, this co-flow micro-combustor model was compared with a proposed cross-flow model of the same length and height and it has been found that the cross-flow model can generate a high energy output along with good combustion efficiency and wall thermal performance for upper range of fuel supplies. This proposed cross-flow model can provide a combustion efficiency of around 93% or more for 10–30 cm3/s fuel supply rate, whereas, the previous validated co-flow model had a very poor efficiency of around 20% before flame blow-out. There are primarily two reasons behind this, one is fuel leakage due to the opening of flame tip and the second is fuel–air mixing quality, which was improved for the cross-flow model.