The paper presents firstly a novel system-on-chip (SoC) architecure consisting of a 32-bit RISC processor, on-chip memory, state-of-the art IPs and embedded full-custom bit serial FPGA(BSFPGA) I/O interface. The system inherits the compatibility of AMBA architecture, the flexibility of BSFPGA, so that it can be used for various types of applications without any additional I/O pins. Example application is to realize fingerprint authentication system in a chip. The paper presents secondly design flow for SoC, including a full-custom block. With RTL model for BSFPGA, it enables a timing simulation of the total system in RTL level and a timing verification in transistor level.