We aimed to estimate cardiac output (CO) from photoplethysmography (PPG) and the arterial pressure waveform (ART) using a deep learning approach, which is minimally invasive, does not require patient demographic information, and is operator-independent, eliminating the need to artificially extract a feature of the waveform by implementing a traditional formula. We aimed to present an alternative to measuring cardiac output with greater accuracy for a wider range of patients. Using a publicly available dataset, we selected 543 eligible patients and divided them into test and training sets after preprocessing. The data consisted of PPG and ART waveforms containing 2048 points with the corresponding CO. We achieved an improvement based on the U-Net modeling framework and built a two-channel deep learning model to automatically extract the waveform features to estimate the CO in the dataset as the reference, acquired using the EV1000, a commercially available instrument. The model demonstrated strong consistency with the reference values on the test dataset. The mean CO was 5.01 ± 1.60 L/min and 4.98 ± 1.59 L/min for the reference value and the predicted value, respectively. The average bias was −0.04 L/min with a −1.025 and 0.944 L/min 95% limit of agreement (LOA). The bias was 0.79% with a 95% LOA between −20.4% and 18.8% when calculating the percentage of the difference from the reference. The normalized root-mean-squared error (RMSNE) was 10.0%. The Pearson correlation coefficient (r) was 0.951. The percentage error (PE) was 19.5%, being below 30%. These results surpassed the performance of traditional formula-based calculation methods, meeting clinical acceptability standards. We propose a dual-channel, improved U-Net deep learning model for estimating cardiac output, demonstrating excellent and consistent results. This method offers a superior reference method for assessing cardiac output in cases where it is unnecessary to employ specialized cardiac output measurement devices or when patients are not suitable for pulmonary-artery-catheter-based measurements, providing a viable alternative solution.