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Do you mean that there is no restriction on the source of pll_ref_clk of the DDR3 hard controller,in other words,the pll_ref_clk can be driven by the clock in FPGA,not must be driven by the clock from the dedicated clock input pins?
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There *ARE* restrictions on the clock input pin (it needs to be a PLL clock input), and there *ARE* further restrictions on the interface actually meeting timing. You need to synthesize a design using Quartus to determine how to meet those requirements. Yes, this takes a little "guesswork", but in general, start with a single DDR controller with a PLL clock input on the same side as the DDR controller pins. If that meets timing, then you have your "golden reference". From that, you can start to change the PLL input clock and see what warnings Quartus generates.
Cheers,
Dave