For spark-ignition direct-injection (SIDI) engines in which fuel is injected directly in the cylinder, large amount of in-cylinder mixture variation on a cyclic basis could adversely influence the combustion quality and lead to more fuel consumption and excessive engine emissions. In this study, multiple cycles of intake air flow fields and their effects on fuel spray structure were investigated experimentally in an optical SIDI engine. Proper orthogonal decomposition (POD) was utilized to identify and quantify the cyclic variations of intake air motions and spray the pattern in the cylinder. Results show that the pattern of POD mode 1 resembles the ensemble-averaged structure of intake air velocity field. Other higher POD modes are useful to identify the fluctuations of the flow. The cycle-to-cycle difference of in-cylinder air flow motion also influences the variations of spray structure on a cyclic basis, which can be unambiguously quantified by analyzing the POD modes 1 and 2 of the spray pattern. Whereas the first mode exhibits the variation for the dominant portion of spray structure, the second mode captures the subtle differences in the positions of discrete fuel spray plumes under the influence of intake air. Overall, POD can be useful in identifying and quantifying the cyclic variations of the intake air motion and spray structure in the cylinder of running engine conditions.