To improve understanding of M−L bonds in 3d transition metal complexes, analysis by energy decomposition analysis and natural orbital for chemical valence model (EDA‐NOCV) is desirable as it provides a full, quantitative and chemically intuitive ab initio description of the M−L interactions. In this study, a generally applicable fragmentation and computational protocol was established and validated by using octahedral spin crossover (SCO) complexes, as the transition temperature (T1/2) is sensitive to subtle changes in M−L bonding. Specifically, EDA‐NOCV analysis of Fe−N bonds in five [FeII(Lazine)2(NCBH3)2], in both low‐spin (LS) and paramagnetic high‐spin (HS) states led to: 1) development of a general, widely applicable, corrected M+L6 fragmentation, tested against a family of five LS [FeII(Lazine)3](BF4)2 complexes; this confirmed that three Lazine are stronger ligands (ΔEorb,σ+π=−370 kcal mol−1) than 2 Lazine+2 NCBH3 (=−335 kcal mol−1), as observed. 2) Analysis of Fe−L bonding on LS→HS, reveals more ionic (ΔEelstat) and less covalent (ΔEorb) character (ΔEelstat:ΔEorb 55:45 LS→64:36 HS), mostly due to a big drop in σ (ΔEorb,σ ↓50 %; −310→−145 kcal mol−1), and a drop in π contributions (ΔEorb,π ↓90 %; −30→−3 kcal mol−1). 3) Strong correlation of observed T1/2 and ΔEorb,σ+π, for both LS and HS families (R2=0.99 LS, R2=0.95 HS), but no correlation of T1/2 and ΔΔEorb,σ+π(LS‐HS) (R2=0.11). Overall, this study has established and validated an EDA‐NOCV protocol for M−L bonding analysis of any diamagnetic or paramagnetic, homoleptic or heteroleptic, octahedral transition metal complex. This new and widely applicable EDA‐NOCV protocol holds great promise as a predictive tool.