In order to study the influencing mechanism of carrageenan oligosaccharide on the muscle quality and protein in Litopenaeus vannamei during F-T cycles, the myofibrillar protein of samples during F-T cycles with different pretreatment methods (sterile distilled water, tripolyphosphate and carrageenan oligosaccharide) were measured respectively by Fourier Transform Infrared (FT-IR) and Micro-Raman (M-Raman). The data of FT-IR and M-Raman for myofibrillar protein in Litopenaeus vannamei with different pretreatments after 0, 2, 4, 6 F-T cycles were collected respectively. The results showed that the destructive effect of F-T cycles on the protein structure in Litopenaeus vannamei could be demonstrated by first-order spectrogram, and the structural changes of protein under different pretreatments could be qualitatively and quantitatively analyzed by second order derivation and gaussian curve fitting. The intensity changes of each characteristic peak at first-order spectrogram in FT-IR and M-Raman were indicated that F-T cycles could aggravate the loss and structural damage of muscle protein in shrimp. The primary chain conformation of secondary structure in the shrimp muscle protein was mainly characterized by amide band Ⅰ (1 600～1 700 cm-1). The results of FT-IR showed that the secondary structure of fresh shrimp protein was mainly β-turn, followed by β-sheet. It could compensate for the insensitivity of β-turn and β-sheet by M-Raman. The amide band Ⅰ of FT-IR and M-Raman spectrum after gaussian fitting qualitatively and quantitatively showed the secondary structure changes of protein during F-T cycles mainly made the decrease of α-helix and the increase of random coil, and carrageenan oligosaccharide pretreatment could significantly inhibit the loss of α-helix in shrimp protein during F-T cycles. FT-IR was not sensitive to the changes in the compositions of amino acid exposed to protein surface, while M-Raman spectra could compensate it to show the changes in protein conformation on side chain. The bands represented that tyrosine residues appeared at 850 and 830 cm-1, and the peak intensity ratio indicated the exposure of tyrosine, which showed an increasing trend during F-T cycles. The C—H bending and stretching vibration of aliphatic side chain amino acid residues were in 1 440～1 465 and 1 465～2 800 cm-1 respectively, and the peak strength changes of 1 448 and 2 935 cm-1 were on behalf of hydrophobic interaction strength of amino acid on side chain, which increased during F-T cycles. The changes in characteristic spectral bands of protein on side chains by M-Raman showed that F-T cycles made the hydrogen bond rupture of protein intramolecular or intermolecular, the exposure of tyrosine or amino acid residues on aliphatic side chain, and carrageenan oligosaccharides pretreatment could slow down the change significantly. Therefore, carrageenan oligosaccharides could delay the rupture of hydrogen bond and exposure of side chain hydrophobic group in muscle protein during F-T cycles, the secondary structure of protein could be further stabilized, the function of protein could be maintained and the quality of shrimp could be improved under F-T cycles. In addition, the innovative combination of FT-IR and M-Raman spectra was applied to the research on the mechanism of carrageenan oligosaccharide for improving the muscle quality under F-T cycles. It was found that FT-IR was more sensitive to the characterization of secondary structure in muscle protein, while M-Raman spectra could provide the theoretical references for the conformation changes of protein on side chains. The combination of them could provide the compatible and complementary information to better analyze the structural changes of protein in samples after different pretreatments.