The power supply modulated microstimulator system can drive an expandable electrode array with reduced heat generation across the current drivers and high stimulation efficiency. Here, we present a comprehensive analytical modelling of the system to investigate internal and external energy flow during biphasic stimulation pulses spanning over varying loading configurations (e.g. number of electrodes, and stimulation current amplitude) that were not covered by existing works on the power supply modulated microstimulators. This paper fills the research gap by presenting the systematic tools for attaining insights of a stimulator system featuring a bidirectional DC-DC converter with an algorithmic digital controller. The models employed here are based on traditional analytical methods such as transfer functions and state-space dynamic models incorporating various circuit elements incurring power loss. With the models, the behaviour and power efficiency under a wide range of parameters associated with stimulator are attained. Numerical assessment reveals that the digital controller can track the output supply voltage at the phase transition boundaries just in tens of switching cycles. The system was also studied on a verification platform, where the internal signals of the digital controller were carefully examined. Measurement results show that the system behavior well matched to the simulation results, demonstrating the effectiveness of the analytical system model for obtaining key insights for generic large-scale micro-stimulator designs.