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I don't know whether it will cause some problem?
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It will. At best, the negative voltage is cut by device internal substrate diodes, but you shouldn't rely on it. The general tool for level conversion is a fast comparator. As I said, not only the signal level, but also the rise time is significant for clocks. Slow edges can bring up double clocking and always introduces higher jitter. The processing of clock signals isn't particularly a FPGA topic, you can't expect detailed suggestions in the Altera literature. You should rather consult datasheets and application notes of fast comparators, e.g. from ADI, TI, Maxim, Linear or National or general electronics text books.
If the clock has sufficient fast edges, a series resistor and schottky diode limiter (connected to GND and VCCIO, either 3.3 or 2.5V) can be a suitable solution.