A pin connection testing system for connector, and a method thereof are disclosed. In the pin connection testing system, a JTAG instruction is used to control a PLD, to drive the demultiplexer to transmit each to-be-tested signal, which is from the connector, to a first line or a second line; and, when the to-be-tested signal is transmitted to the first line, the to-be-tested signal is converted from analog to digital and encoded, and then transmitted to I/O pins of the PLD for reading; and, when the JTAG command is transmitted to the second line, the PLD reads the statuses of the I/O pins electrically connected to the second line; and then the PLD generates a test result according to the to-be-tested signals and the read I/O pins. Therefore, the technical effect of improving convenience in testing the connection status of the connector can be achieved.