Four spin-crossover (SCO) complexes with general formulae, [M-2(CH3COO)(4)(L)(2)] and [M(L)(3)](BF4)(2), where M = Fe(II) and Co(II), containing extended pi-conjugated bipyridyl ligand and N-3-Schiff bases appended with linear C16 carbon chains at the N atoms were successfully synthesized and characterized. Correlation of its structural properties to thermoelectric behavior is investigated: (1)structure of complexes, (2)choice of metal centre and (3)choice of counter ions. It was found that the structure of the molecule, i.e. molecular versus ionic has the largest impact on the SCO behavior. We found that the molecular complexes with higher percentage of high-spin (73.4% HS for Fe-dinuc and 78% HS for Co-dinuc) have produced the highest Seebeck values in mV K-1 (-0.57 +/- 0.01 for Fe-dinuc and -0.58 +/- 0.01 for Co-dinuc) due to the weaker metal-to-ligand bonds resulting in the increase mobility of the I- during agglomeration formed, thus increased the entropy in the solution. Additionally, choice of metal centre also was a factor to determine the magnitude of Seebeck performance due to the spin state transition during electron transfer. For counter ion effect, it has the effect of determining the sign of the Seebeck value where I- is easier to oxidize/reduce process compared to CH3COO- and BF4- due to lower redox potential. These findings will assist in a systematic molecule design pathway for high potential SCO complexes for thermoelectric applications.