Taking six typical associated ore waste samples as the research object, the thorium content in the samples was determined by spectrophotometry and the factors affecting the test results were analyzed. Three factors that may obviously affect the accuracy of the results were selected and optimized the experimental conditions by controlling variates, and the results were compared with inductively coupled plasma mass spectrometry and gamma spectrometry to prove the reliability of the optimization method. The results showed that the main affecting factors in the sample were the digestion frequency, colorimetric time, and residual extractant. The detection accuracy and efficiency of thorium in the six typical associated ore residues were improved by increasing the digestion frequency to 3 times, ensuring a colorimetric time of 3 min to 5 min, and adding hydrogen peroxide and perchloric acid to remove the extractant.