God is omniscient, which means that He knows our thoughts, but He also knows the intent (or lack of intent) behind them (1 Chronicles 28:9; Psalm 10:4; Psalm 139:2; Hebrews 4:12). If we are struggling to manage our overwhelming thoughts, we can ask God to search us (Psalm 139:23-24) as well as console us (Psalm 94:19). Instead of letting our intrusive thoughts cause us unnecessary anxiety or letting them control our actions, we should take every thought captive by methodically testing them against God’s Word (2 Corinthians 10:3-5). We should also focus on what we are putting in our minds. We can do this by testing and aligning our thoughts according to Philippians 4:8.
An intrusive thought is an involuntary, unwanted image, phrase, or impulse. They are very common; nearly everyone has them from time to time. Sometimes they are of a violent nature, other times they are sexual. Often, they are blasphemous or induce great fear of having done a ritual incorrectly. They can be quite disconcerting, especially when they are completely contrary to what a person actually believes.
To help with our intrusive thoughts, we should be aware of God’s character and test every intrusive thought against God’s Holy Word. We must also be very careful about what we are putting into our minds. We should guard our eyes, since they are the “lamp to the body” (Matthew 6:22) as well as put in our minds godly things as highlighted in Philippians 4:8.
Sometimes repeatedly capturing the thought and refuting it with God's Word doesn't make the thought stop because intrusive thoughts can be overwhelming and impossible to control. This is one of the primary symptoms of obsessive compulsive disorder and a lesser symptom of many other disorders. [like what? Either name a couple or eliminate the phrase “and a lesser symptom…”.] If the intrusive thoughts are particularly debilitating, we should see a medical doctor or a qualified counselor. God has provided us with physicians who can care for the body as well as those who care for the soul, and we should take advantage of their expertise.
No matter how much turmoil we feel over our intrusive thoughts, God understands us (Psalm 139:2) loves us very much (1 John 4:16) and is the Giver of incredible peace (John 14:27).