hi;
last months i design an at91sam9g45 board . i can use JTAG to download code to at91sam9g45 's internal ram and run .but i find xin32 32.768k can not work ,12Mhz work ok. ALL core,IO voltage is ok.i want to know why?

With the limited information provided we are left to guess. Assume we know nothing about your design beyond what you have actually written/provided.

Is it wired correctly, do you are a circuit diagram for the oscillator section?
Crystal or Oscillator?
Is it a suitable part, with the correct capacitance/loading?
Not working, how? Is it not Starting? XIN/XOUT what voltages?
Have you enabled it correctly?

From the manual

8.6.1 Switch from Internal RC Oscillator to the 32768 Hz Crystal
To switch from internal RC oscillator to the 32768 Hz crystal, the programmer must execute the
following sequence:
• Switch the master clock to a source different from slow clock (PLLA or PLLB or Main
Oscillator) through the Power Management Controller.
• Enable the 32768 Hz oscillator by setting the bit OSCEN to 1.
• Wait 32768 Hz startup time for clock stabilization (software loop).
• Switch from internal RC to 32768 Hz by setting the bit OSCSEL to 1.
• Wait 5 slow clock cycles for internal resynchronization.
• Disable the RC oscillator by setting the bit RCEN to 0.