To build an integrated battery charger with multiple functions for electric vehicles (EVs), the system normally has several stages, such as AC/DC power factor conversion (PFC) converter, isolated and/or non-isolated DC/DC converters. Therefore, it is important to implement the start-up and shutdown procedure by coordinating multi-stage converters to avoid potential large inrush current or over voltage. This paper firstly proposed a highly integrated multi-stage battery charger for electric vehicles that offers multiple functions, including on-board charger (OBC), vehicle-to-load (V2L), wireless power transfer (WPT), all using a 400V battery, and auxiliary power module (APM) for a 12V battery. The control methods for each function are introduced. Based on the system configuration and characteristics of different functions, comprehensive system-level start-up and shut-down schemes are proposed for practical operation scenarios of OBC, WPT and V2L. Finally, a 400VAC/800VDC/22kW prototype is built and the effectiveness of the proposed start-up and shut-down schemes is verified by experiments.