Hello,
What is the flash erase and write operation time of mpc5744p?
Please have a look at datasheet for it: 3.16.1.1 Flash memory program and erase specifications

In addition, when I do a project of Program bootloader , the upper computer can send 1.5MB files within 80s, but it takes more than 3 minutes to complete the whole Program / download process. What is the reason?
This depends on how do you program the device. For some serial communication it depends on settings and HW limits or for JTAG / NEXUS it depends on programmer spec, etc... there can be lot of delays.
Best regards,
Peter