I can program .sof by programmer, but I can’t program .pof by programmer. Why? What would cause this problem?

Without you telling us specifically about the board you have (development board, custom design, ...?) and what devices are on the board (FPGA, config eeprom) you will not get much help.

As a general rule, if you ask questions here you need to provide as much background info as you can (as Vicky says) or else no one can help you.