In the past several decades, the rapid development of aquaculture has brought many environmental problems. The waste discharged from aquaculture may lead to eutrophication and deterioration of water quality, which will further affect the growth and health of aquatic animals. A new aquaculture model is emerging to deal with this problem, named in-pond “raceway” aquaculture system. Based on that, a comparative study on the nutritional value and volatile flavor compounds profile in muscle of Culter alburnus was conducted to investigate the difference between in-pond “raceway” aquaculture system and traditional pond culture. Amino acids analyzer, high performance liquid chromatography (HPLC) and gas chromatograph-ion mobility spectrometer (GC-IMS) were used to identify and analyze the profile of amino acids, fatty acids and volatile flavor compounds in the muscle under different culture conditions. The fingerprint spectra of volatile flavor compounds were established. There was no significant difference in the content of crude protein and crude lipid of muscle between the two groups. The content of essential amino acids [EAA, (8.54±0.01) g/100 g wet basis] and total amino acids [TAA, (17.36±0.00) g/100 g wet basis] of muscle in the in-pond “raceway” group was significantly increased. Additionally, a total of 23 volatile flavor compounds were screened from the C. alburnus muscle from the two groups. Compared with the traditional pond culture group, the contents of butanal, 3-methylbutanal, 2-methylbutanal, pentanal, heptanal, benzaldehyde, octanal, nonanal, 2-butanone, 3-hydroxy-2-butanone and ethanol were decreased, while the contents of 2-heptanone, 1-hexanol and 1-octen-3-ol were increased in the in-pond “raceway” aquaculture system group. At the same time, compared with traditional pond culture group, the volatile flavor of the in-pond “raceway” aquaculture system group improved due to the decrease of some unpleasant volatile flavor compounds. C. alburnus cultivated in the in-pond “raceway” aquaculture system improved the amino acid and flavor characteristics and kept the muscle approximate composition unchanged. The above results provide basic data for the evaluation of the flesh quality of C. alburnus of the in-pond “raceway” aquaculture system, which indicates that this model has great potential for improvement of fish quality.