Having your intellect rule over your nature is an essential obligation. Your intellectual realizations should be so strong that they are able to overcome natural tendencies and habits. If you let your natural tendencies rule you, you are likely to make many serious mistakes in life.
Keep in mind that this is an ideal, and it is unrealistic to demand perfection of oneself. The goal should be improvement. A person who works on his power of thinking for many years will eventually reach high levels of expertise. But do not demand of yourself instantaneous perfection for this will needlessly cause guilt feelings and anxiety.
Today, set yourself a small, realistic, attainable goal.
(see Rabbi Yosef Leib Bloch; Shiurai Daas 3:40; Gateway to Happiness, p.67)