"One thought" refers to the mind which is completely clear and free from attachment. "Ten thousand years" is simply a very long time without interruption. We can read similar passages in later descriptions of Silent Illumination.
Master Shih-shuang Ch'ing-chu 石霜慶諸(805-888) lived on a mountain called Shih-shuang for 20 years. His disciples just sat continually, even sleeping in the upright position. In their stillness, they looked like so many dead tree stumps, that they were named "the dry wood sangha." Shih-shuang has two famous phrases of advice. One was, "To sit Ch'an, fix your mind on one thought for ten thousand years." The other was, "Let yourself be like cold ashes, or like dry wood."
Hung-chih himself studied for a while with Master K'u-mu Fa-ch'eng 枯木法成. He was called K'u-mu (dry wood) because when he sat, his body resembled a block of dry wood. In the hands of Hung-chih, this practice evolved into what he called Silent Illumination. He describes "silent sitting" thus: "Your body sits silently; your mind, quiescent, unmoving. This is genuine effort in practice. Body and mind are at complete rest. The mouth so still that moss grows around it. Grass sprouts from the tongue. Do this without cease, cleansing the mind until it gains the clarity of an autumn pool, bright as the moon illuminating the evening sky."