Thermal pasteurization decreases the sensory quality of mandarin juice. Flavor composition was determined in four fresh-squeezed and heat-processed mandarin juice varieties using molecular sensory science approaches. The relationships between odorants and sensory profiles were analyzed, and markers for flavor deterioration were screened by multivariate statistical analysis. Seventy-four volatiles were identified, among which 36 odorants with flavor dilution factors ranging from 2 to 128 were detected by multidimensional gas chromatography-mass spectrometry/olfactometry (MDGC-MS/O) coupled with aroma extract dilution analysis (AEDA). Higher intensities of cooked and off-flavor notes were observed in the heated mandarin juice, which was related to the concentration changes of the methional, methanethiol, dimethyl sulfide, and carbon disulfide by partial least squares (PLS) analysis. Ten potential markers (methional, methanethiol, dimethyl sulfide, hydrogen sulfide, β-damascenone, camphene, trans-β-ionone, decanal, d-limonene, and α-pinene) were responsible for the sensory discrimination of fresh-squeezed and heated mandarin juices.