Problem solved.Flash in stock 6.0 firmware; boot into fastboot mode and load TWRP (3.0.2) with /system READ ONLY mode. I think this is the cause for the failure; Install SuperSU (2.7.9-SR3). And saw a message "System-less mode. Boot image support required." on terminal. What does "boot image support reqiured" means? Reboot and SuperSU works like a charm.
Update: I've tried to boot TWRP without /system write protection and flash in SuperSU 2.79-SR3 successfully. So only the SuperSU is responsible for this issue?