I Want to design a project with ISP Chip.
Good for you but 89c53 is not a SERIAL ISP chip. Use Philips P89C51Rx2 or P89C66x or one of the Atmel ISP derivatives (careful, Atmel call some chips ISP that are not SERIAL ISP chips)

1) when I Program it, I Need a supplies, how do I Make sure that the entier circuit will not work at the programming process?
No, you do not need any 'supplies' all that is required is that your setup has a true RS232 port. I do not know about Atmel, but for Philips, the ISP code is in a separate ROM so your code in flash will definitely not run during ISP.

2) How can I use all the PORT Pins, If those are used to program the CHIP ?
For SERIAL ISP chips such as those listed above, no port pins are involved, just the UART pins. OK, a small caveat, for the Philips chips (Atmel also?) you may not pull p2.6 and p2.7 low during programming.

3) Do I Need to change the CRYSTAL for programming ?
NO, but as always, the thing works best when the crystal frequency is chosen for the UART, not the CPU.

Download the Philips AN416, that will show you what SERIAL ISP looks like.

Erik

PS ISP other than serial ISP is a joke.