God knows our thoughts, as well as the intention of our thoughts. God knowing our thoughts is a comfort because of His great love for us.
Our thoughts are one of the most private things that we have as humans. Unless we speak outright about them, there is no way for anyone else to know our thoughts. Often, this gives us a sense of security and safety regarding the things we think. However, there is one Person who knows our thoughts and loves us anyway. There is nothing God does not know, nowhere that He is not, and nothing that He cannot do (Psalm 139)! We should not fear sharing our thoughts with God because He already knows them (1 Chronicles 28:9; Psalm 91:15; Ephesians 4:22–32).
In Isaiah 55:8, the prophet Isaiah writes, "For my thoughts are not your thoughts, neither are your ways my ways, declares the LORD." God thinks and acts in ways that exceed our human imagination. God does not need to learn or be taught anything because He is perfect in every way (Psalm 18:30; 1 John 3:20). God is our teacher, and through His Word, we can come to know Him and His ways (John 13:13). He knows the end from the beginning and the answer to all of the whys that we face (Isaiah 46:10). None of our thoughts are too much for God to handle.
Instead, He knows our thoughts, can handle our thoughts, and is the One who helps transform our thoughts (Romans 12:2). It may sound frightening to some that God knows everything we think, but God promises us grace and mercy (Ephesians 2:8–9; Titus 2:11; Hebrews 4:16; 1 John 1:9). He is not interested in our thoughts in order to trip us up but in order to build an intimate relationship with us through Jesus Christ. No matter who we are, what we do, or where we go, God continues to seek our hearts, especially those who proclaim that He is Lord (Deuteronomy 4:39; Proverbs 3:1; Romans 10:9; Philippians 2:11)!
If we have accepted that we are sinners and have believed that Jesus died and rose again, then we should also be comforted that we have a Father who loves us and knows us more than we could ever love or know ourselves. Far from being afraid that God knows our thoughts, we can be comforted at the depth of His knowledge of us and the magnitude of His love for us. First John 3:20 encourages, "for whenever our heart condemns us, God is greater than our heart, and he knows everything."