Ultrasound imaging is a first-line diagnostic method for screening the thrombus. During thrombus aging, the proportion of red blood cells (RBCs) in the thrombus decreases and therefore the signal intensity of B-scan can be used to detect the thrombus age. To avoid the effect of system gain on the measurements, this study proposed using the empirical mode decomposition (EMD) of ultrasound image as a strategy to classify newly formed and aged thrombi. Porcine blood samples were used for the in vitro induction of fresh and aged thrombi (at hematocrits of 40%). Each thrombus was imaged using an ultrasound scanner at different gains (15, 20, and 30 dB). Then, EMD of ultrasound signals was performed to obtain the first and second intrinsic mode functions (IMFs), which were further used to calculate the IMF-based echogenicity ratio (IER). The results showed that the performance of using signal amplitude of B-scan to reflect the thrombus age depends on gain. However, the IER is less affected by the gain in discriminating between fresh and aged thrombi. In the future, ultrasound B-scan combined with the EMD may be used to identify the thrombus age for the establishment of thrombolytic treatment planning.