“If our heart condemns us, God is greater than our heart, and knows all things. Beloved, if our heart does not condemn us, we have confidence toward God” (1 John 3:20-21).
The context concerns love. John has instructed, “My little children, let us not love in word or in tongue, but in deed and in truth” (1 John 3:18). The reader is to examine himself (cf. 2 Corinthians 13:5). Can he, in good conscience, say that he so loves his brethren? If no, remember that you have a greater, all-knowing One, to whom you will give account one day (cf. 1 Corinthians 4:4). If yes, then one can have confidence in his relationship with God (1 John 3:21 cf. 4:17-18).
This is not suggesting that the heart (conscience) is always a perfect or a safe guide. It is not (cf. Proverbs 16:2; 16:25; Acts 26:9; 1 Corinthians 4:4).
However, man has a conscience. He should conscientiously examine his life in light of the Scriptures (2 Corinthians 13:5). He should seek to live according to the Scriptures with a pure conscience (cf. 1 Timothy 1:18-19; 3:9; 2 Timothy 1:3).
One might think of the conscience as a “warning light.” God has created a “warning light” with in us. The word “conscience” literally means “with knowledge.” Strong’s indicates that it is some times used to mean “co-perception, i.e. moral consciousness.” Vine’s indicates that it is used of “(a) the sense of guilt before God” and “(b) that process of thought which distinguishes what it considers morally good or bad, commending the good, condemning the bad, and so prompting to do the former, and avoid the latter.” The conscience warns based on the information which has been inputted. If inputted with correct information, it provides a reliable warning. We are to be warned by scripture (cf. Psalm 19:11). The conscience relies on what knowledge one has [Notice the word “knowledge” (1 Corinthians 8:7, 10); Also see: Hebrews 5:12-14, and Romans 12:1-2 (cf. “renewed” Ephesians 4:20-24)]. The conscience can be misguided, and misinformed (Acts 26:9; 1 Corinthians 8:7),
One might think of the conscience as an “inner judge.” Think of a courtroom. (1) The witnesses and the evidence are provided by the intellect and knowledge of man. (2) The lawyers are the emotions and reasoning for and against something in one’s head. (3) The judge who tries to make sure that the case is decided fairly based on the law is the conscience. (4) The jury who renders the verdict is one’s ultimate will or volition (This comparison is provided by Kerry Duke, God at a Distance, pp. 112-115). It is possible to render a decision which goes against one’s conscience and what one knows to be right (e.g. John 12:42-43; Romans 14:23; 1 Corinthians 8:10).