Manifold micro pin-fin heat sink (MMPFHS) is one of the promising thermal management approaches to fulfil the heat dissipation requirements of high flux density electronics. The various spatial arrangements and morphologies of the micro pin-fins are proposed in this paper for further improving the thermal performance of MMPFHSs. The flow characteristics and heat transfer performance are numerically investigated and comparatively evaluated under similar conditions. The results show that the additional upper micro pin-fins regulate the flow in the spatial dimension and also enhance the heat transfer in comparison with the arrangement of only the lower pin-fins. With the same porosity, varying the micro pin-fin morphologies has little effect on the pumping power in the model with the additional upper micro pin fins, but the conical pin-fin has the best temperature homogeneity. And the larger volume of the lower pin-fin results in better heat transfer. When the volume ratio (lower pin-fin volume/ upper pin-fin volume) changes from 0.4 to 1.4, the maximum bottom surface temperature decreases by 20.31%. The lower porosity causes better heat transfer performance at the same volume ratio. Under the "C1" type arrangement no matter the upper or lower pin-fin, when its height is greater than 250 µm, the maximum temperature at the heating surface can be further reduced, and the upper pin-fin in the shape of the frustum of a cone is more effective in heat transfer.