Hello @haihui.pang,
Please try the following:
- Flash your eMMC device with the base image (prior to loading your application) and boot the Jetson
 - Insert the SD Card, format it and create an ext4 partition
 - Mount your SD card and copy the rootfs into it (for example, like in this post linked here)
 - Change the extlinux.conf file under /boot/extlinux. In the APPEND entry, replace root=/dev/mmcblk0p1 by your SD card partition.
 - Reboot
 
By then, the bootloader should be able to boot from the SD Card so you can the load your application.