We constructed a reasonable healthcare monitoring system with pulse wave and respiratory analysis to assess blood vessel conditions and the autonomic function in daily life. Filter circuits with an infrared sensor were carefully designed to complete the peripheral pulse wave measurement and analysis, considering individual differences to a pulse sensor and the potential for the system to be used as wearable devices and applications. The analyzer for our system is capable of predicting arterial states and stiffness. A user interface with a respiratory pacemaker can assist voluntary breathing, visualize pulse wave features, and regulate them in real time. The user interface software is widely compatible and could be easily applied to mobile healthcare devices. We also evaluated how respiration control reflected pulse rate variability [i.e., fluctuations in peak-to-peak intervals (PPI)] associated with the autonomic nervous system. An experimental study under various breathing rates was performed using the created user interface with a respiratory pacemaker. The transfer gain of the PPI caused resonance at the respiratory rate of 0.1 Hz (p < 0.5), corresponding to the sufficiently stimulated vagal tone of the heart. A simulation study revealed that the fuzzy inference indicates the robustness of respiratory regulation to maximize the amplitude of PPI oscillations under the inclusion of individual difference and unexpected response. As future perspective, the respiratory pacemaker used to regulate the pulse wave feature could be applied to an effective recovery support system especially under blunted autonomic function such as during mental stress and hypoxia.