Q:

How to flash a lot of devices like Raspberry Pi (More than 1000)? 

Our devices based on ARM and eMMC memory on board, and how mass flash our soft on this devices? ( More than 1000 devices)

A:

In manufacturing.  You would provide the code to be flashed on the on board flash prior to assembly, or it would be loaded through a jtag jig after assembly. 
For an end user, there are options like getting SD cards manufactured with your software on it, then loading those on the devices yourself (or a middle man service that you pay to do this), or using software like PXE network booting that will install it for you after configuration.  Different devices have different methods.  The RPI 2 needs a sd card with config to boot to network boot, the 3 requires a one time config, and the 1 cannot natively network boot.