Pulsating air supply combined with stratum ventilation has the potential to improve thermal comfort on the premise of ensuring good energy efficiency and indoor air quality. An indoor three-dimensional transient computational fluid dynamics (CFD) model for pulsating air supply combined with stratum ventilation was established and verified, and 26 simulation cases were calculated. Based on the dynamic thermal comfort evaluation indexes verified by experiments, namely the time-averaged predicted mean vote (TAPMV) and time-averaged percentage of dissatisfied due to draft (TAPD), the influences of various parameters of the pulsating air supply function (i.e., total period duration, ratio of the high-velocity duration to the low-velocity duration, and air supply velocity) on thermal comfort were investigated. One of the multi-criteria optimization methods, i.e., Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) was used. It was found that, when the total cycle duration was 300 s, the ratio of the high-velocity duration to the low-velocity duration was 1, the air supply velocity of the high-velocity duration was 1.95 m/s, and the air supply velocity of the low-velocity duration was 1.05 m/s, the comprehensive evaluation of thermal comfort is the best.