A control system for variable rate fertilization, which depends on deep-fertilization liquid fertilizer applicator, was introduced. The single chip microcomputer was used as core processor and electromagnetic proportion regulator valve was used as execution unit. Software was designed for selecting data and sending commands. The test results in the test-bed showed that the system can complete the control of variable rate fertilization and the error of the variable fertilizing was less than 0.5 mL in each time, which meets the liquid fertilizer variables requirement. 