Engine-out CO emission was measured over a wide range of swirl ratios and injection timings on low-temperature diesel combustion regime in a small-bore single-cylinder diesel engine. Our previous work has shown that late-cycle mixing plays an important role even in so-called dilution-controlled low-temperature combustion systems. In this study, we employ multi-dimensional numerical simulation to characterize the flow structures and their impact on CO emissions. 65% exhaust gas recirculation is simulated with additional N2 and CO2. The CO emission shows optimal values at swirl ratio of 2.59 and limited ranges of injection timings. The numerical simulations show that the formed CO is trapped inside bowl at high swirl of 7.12, while CO is lifted out due to an enhanced reverse squish flow with a swirl ratio of 2.59. For a lower swirl ratio of 1.44, the existence of a single, large bulk flow structure limits the mixing process. The measured fuel conversion efficiency shows maximum value at low swirl ratio. The source of the maxima is clarified by the analysis of the work conversion efficiency. combustion etliciency, and heat transfer loss. Results show heat loss plays important role in determining the fuel conversion elficiency.