It is important to identify non-planar deformations of porphyrin macrocycle in metallo-porphyrin proteins due to their functional relevance. The relationship between non-planar deformations of porphyrin macrocycle and low frequency Raman spectral bands of Ni(II) meso-tetraphenyl porphyrin (NiTPP), with different coordination numbers, was studied by density functional theory (DFT), normal coordinate structural decomposition method and Raman experiments. The results show that the crystal of four-coordinate NiTPP has two major kinds of non-planar deformations: ruffling and saddling. The non-planar deformations of ruffling and saddling for NiTPP are 1.473 Å and 0.493 Å determined by DFT calculation. The ruffling and saddling deformations can be identified by using the low frequency Raman characteristic peaks (γ12, γ13) and (γ16, γ17), respectively. When four-coordinate NiTPP is transformed to the six-coordinate bis(pyrrolidine) NiTPP (NiTPP(Pyr)2), the large non-planar distortion of the porphyrin macrocycle almost disappears, with the non-planar deformation of saddling only about 0.213 Å estimated by DFT calculation. Experimentally, we can make use of the characteristic peaks of low frequency Raman spectra to identify the saddling deformation beyond 0.25 Å.