Objective: Autonomic function during deep breathing (DB) is normally scored based on the assumption that the heart rate is synchronized with the breathing. We have observed individuals with subtle arrhythmias during DB where autonomic function cannot be evaluated. This study presents a novel method for analyzing cardiorespiratory synchronization: feature-based analysis of the similarity between heart rate and respiration using principles of hyperdimensional computing. Methods: Heart rate and respiration signals were modeled using Fourier series analysis. Three feature variables were derived and mapped to binary vectors in a high-dimensional space. Using both synthesized data and recordings from patients/healthy subjects, the similarity between the feature vectors was assessed using Hamming distance (high-dimensional space), Euclidean distance (original space), and with a coherence-based index. Methods were evaluated via classification of the similarity indices into three groups. Results: The distance-based methods achieved good separation of signals into classes with different degree of cardiorespiratory synchronization, also providing identification of patients with low cardiorespiratory synchronization but high values of conventional DB scores. Moreover, binary high-dimensional vectors allowed an additional analysis of the obtained Hamming distance. Conclusions: Feature-based similarity analysis using hyperdimensional computing is capable of identifying signals with low cardiorespiratory synchronization during DB due to arrhythmias. Vector-based similarity analysis could be applied to other types of feature variables than based on spectral analysis. Significance: The proposed methods for robustly assessing cardiorespiratory synchronization during DB facilitate the identification of individuals where the evaluation of autonomic function is problematic or even impossible, thus, increasing the correctness of the conventional DB scores.