State of charge (SOC) and state of health (SOH) of batteries are the indispensable control decision variables for online energy management system (EMS) in modern internal combustion engine vehicles. The real-time and accurate determination of SOC and SOH is essential to the reliability and safety of EMS operation. Obtaining good accuracy for the SOC estimation is difficult without considering SOH because of their coupling relationship. Although several works on the joint estimation of SOC and SOH of lithium–ion batteries are available, these studies cannot be applied to lead–acid batteries because of the differences in physical structure and characteristics. This study handles the problem of modeling the relationship between SOC and SOH of lead–acid battery and their online collaborative estimation. First, the structure and control strategy of a bus-based EMS is discussed, and the improper energy control actions of EMS due to the inaccurate SOC estimation are analyzed. Second, an instantaneous correlation factor β for SOC and SOH is defined as a new state estimating variable, and the simplified linear relationship model between β and open circuit voltage is established through the battery experiments. Third, a discretized augmented system equation of β is deduced according to the relationship model and the Randles circuit model. The least square circuit parameter identification (LSCPI) algorithm is presented to identify the time-varying circuit model parameters, while the adaptive Kalman filter for augmented system (AKFAS) algorithm is employed to estimate β online. A collaborative estimation algorithm is proposed on the basis of the LSCPI and AKFAS to determine SOC and SOH of lead–acid battery in real time, and a demo intelligent battery sensor is developed for its implementation. The results of battery charging and discharging experiments indicate that the proposed method has high accuracy. The estimation accuracy of SOC of this method reaches 3.13%, which is 7% higher than that of the existing method.