Chronic obstructive pulmonary disease (COPD) is one of the most prevalent lung diseases worldwide. COPD patients show major dysfunction in cardiac autonomic modulation due to sustained hypoxaemia, which has been significantly related to higher risk of cardiovascular disease. Obstructive sleep apnoea syndrome (OSAS) is a frequent comorbidity in COPD patients. It has been found that patients suffering from both COPD and OSAS simultaneously, the so-called overlap syndrome, have notably higher morbidity and mortality. Heart rate variability (HRV) has demonstrated to be useful to assess changes in autonomic functioning in different clinical conditions. However, there is still little scientific evidence on the magnitude of changes in cardiovascular dynamics elicited by the combined effect of both respiratory diseases, particularly during sleep, when apnoeic events occur. In this regard, we hypothesised that a non-linear analysis is able to provide further insight into long-term dynamics of overnight cardiovascular modulation. Accordingly, this study is aimed at assessing the usefulness of sample entropy (SampEn) to distinguish changes in overnight pulse rate variability (PRV) recordings among three patient groups while sleeping: COPD, moderate-to-severe OSAS, and overlap syndrome. In order to achieve this goal, a population composed of 297 patients were studied: 22 with COPD alone, 213 showing moderate-to-severe OSAS, and 62 with COPD and moderate-to-severe OSAS simultaneously (COPD+OSAS). Cardiovascular dynamics were analysed using pulse rate (PR) recordings from unattended pulse oximetry carried out at patients’ home. Conventional time- and frequency- domain analyses were performed to characterise sympathetic and parasympathetic activation of the nervous system, while SampEn was applied to quantify long-term changes in irregularity. Our analyses revealed that overnight PRV recordings from COPD+OSAS patients were significantly more irregular (higher SampEn) than those from patients with COPD alone (0.267 [0.210–0.407] vs. 0.212 [0.151–0.267]; p < 0.05) due to recurrent apnoeic events during the night. Similarly, COPD + OSAS patients also showed significantly higher irregularity in PRV during the night than subjects with OSAS alone (0.267 [0.210–0.407] vs. 0.241 [0.189–0.325]; p = 0.05), which suggests that the cumulative effect of both diseases increases disorganization of pulse rate while sleeping. On the other hand, no statistical significant differences were found between COPD and COPD + OSAS patients when traditional frequency bands (LF and HF) were analysed. We conclude that SampEn is able to properly quantify changes in overnight cardiovascular dynamics of patients with overlap syndrome, which could be useful to assess cardiovascular impairment in COPD patients due to the presence of concomitant OSAS.