In the present study, we propose a new surrogate model, called common kernel-smoothed proper orthogonal decomposition (CKSPOD), to efficiently emulate the spatiotemporal evolution of fluid flow dynamics. The proposed surrogate model integrates and extends recent developments in Gaussian process learning, high-fidelity simulations, projection-based model reduction, uncertainty quantification, and experimental design, rendering a systematic, multidisciplinary framework. The novelty of the CKSPOD emulation lies in the construction of a common Gram matrix, which results from the Hadamard product of Gram matrices of all observed design settings. The Gram matrix is a spatially averaged temporal correlation matrix and contains the temporal dynamics of the corresponding sampling point. The common Gram matrix synthesizes the temporal dynamics by transferring POD modes into spatial functions at each observed design setting, which remedies the phase-difference issue encountered in the kernel-smoothed POD (KSPOD) emulation, a recent fluid flow emulator proposed in Chang et al. (2020). The CKSPOD methodology is demonstrated through a model study of flow dynamics of swirl injectors with three design parameters. A total of 30 training design settings and 8 validation design settings are included. Both qualitative and quantitative results show that the CKSPOD emulation outperforms the KSPOD emulation for all validation cases, and is capable of capturing small-scale wave structures on the liquid-film surface faithfully. The turbulent kinetic energy prediction using CKSPOD reveals lower predictive uncertainty than KSPOD, thereby allowing for more accurate and precise flow predictions. The turnaround time of the CKSPOD emulation is about 5 orders of magnitude faster than the corresponding high-fidelity simulation, which enables an efficient and scalable framework for design exploration and optimization.