The invention relates to the field of related clock error compensation technology, and in particular relates to a clock-temperature-error compensation method and a system thereof. The clock-temperature-error compensation method comprises the following steps of: measuring the temperature at initial time, obtaining and storing a first temperature value, and storing the first temperature value; after measuring time T, measuring the temperature again and obtaining a second temperature value; adopting the first temperature value or the second temperature value as the measuring temperature, and according to the relation between the measuring temperature and the clock crystal-oscillator error, calculating and obtaining an error value of a clock; calculating a clock error of the measuring time T; repeatedly executing the steps from step 2 to step 4, till the clock error accumulated value is larger than a preset clock adjusting threshold, adding the value same as the clock adjusting threshold for the clock, and executing the steps from step 2 to step 4 again. The clock-temperature-error compensation method has the advantages that the clock compensation can be realized only by using the common circuit and algorithm without needing to use GPS or a function clock chip with expensive price and adjustable oscillating circuit frequency, so that the production cost is greatly reduced.