We have combined temperature dependent local structural measurements with first principles density functional calculations to develop a three dimensional local structure model of the misfit system [Ca2CoO3][CoO2]1.61 (referred to as Ca3Co4O9) which has a rock salt structure stacked incommensurately on a hexagonal CoO2 lattice. The local structural measurements reveal a low coordination of Co(2)-O bonds in the rock salt layer with large static structural disorder. The temperature dependence of the Co(1)-Co(1) bond correlations in the CoO2 layer are found to be normal above ~75K and with a very small static disorder component. An anomalous enhancement in the Co(1)-Co(1) correlations occurs at the onset of long-range magnetic order. Density functional computations suggest that the reduction of the coordination of Co(2) is due to the formation of chains of Co(2)Ox in the a-b plane linked to the Ca-O layers by c-axis Co(2)-O bonds. The reduced dimensionality introduced by the chain-like structure in the rock salt layer and high atomic order in the C
