Question: God is holy and dwells apart from man in a holy place. How, then, can the Holy Spirit indwell the human heart? My heart is not pure; I am a believer and serve the Lord Jesus Christ, but I am still a sinner. I am not holy. Only God is.
Response: Certainly God is holy, but according to Jesus, “If a man love me, he will keep my words: and my Father will love him, and we will come unto him, and make our abode with him” (Jn:14:23). Jesus, as our great High Priest, was “holy, harmless, undefiled, separate from sinners, and made higher than the heavens” (Heb:7:26), yet God “was made flesh, and dwelt among us” (John:1:14). God dwells among men. He says so.
You ask how the Holy Spirit may indwell a human heart. When Jesus began preparing His apostles prior to His death on the Cross and subsequent departure from them, He said, “I will pray the Father, and he shall give you another Comforter, that he may abide with you for ever” (Jn:14:16). Where will He abide? According to 2 Corinthians:1:22, God “hath also sealed us, and given the earnest of the Spirit in our hearts.” That is His promise to every believer.
Our Lord came and lived in the “midst of a crooked and perverse nation” (Phil:2:15) and did so without sin (Heb:4:15; 1 Pt 2:22). Remember, He was “holy, harmless, undefiled...” (Heb:7:26), yet that same Jesus in Revelation:3:20 said clearly that “Behold, I stand at the door, and knock: if any man hear my voice, and open the door, I will come in to him, and will sup with him, and he with me.” Paul preached to the unsaved men on Mars Hill and told them plainly, “He be not far from every one of us” (Acts:17:27).
You say your heart is not pure, yet Scripture promises, “If any man be in Christ, he is a new creature: old things are passed away; behold, all things are become new” (2 Cor:5:17). There is a solution for the believer who sins: “If we confess our sins, he is faithful and just to forgive us our sins, and to cleanse us from all unrighteousness” (1 Jn:1:9). If you are “a believer,” do you believe that we are holy, cleansed, and made perfect in God’s sight? Does He “cleanse us from all unrighteousness?”
Yes, there is a struggle, as old habits die hard. But remember the promise of Scripture: “For whom he did foreknow, he also did predestinate to be conformed to the image of his Son” (Romans:8:29). Ephesians:2:10 tells us, “For we are his workmanship, created in Christ Jesus unto good works, which God hath before ordained that we should walk in them.” (See also Rom:12:1-2; 1 Pt 1:13-16)
John explained that “if we walk in the light, as he is in the light, we have fellowship one with another, and the blood of Jesus Christ his Son cleanseth us from all sin” (1 Jn:1:7).
Paul encouraged the Corinthians, “For the love of Christ constraineth us; because we thus judge, that if one died for all, then were all dead: And that he died for all, that they which live should not henceforth live unto themselves, but unto him which died for them, and rose again” (2 Cor:5:14-15).
The Holy Spirit indwells the human heart because of the finished work of Christ, not by our merit. It is He who “purifies” our hearts. Ephesians:2:13 tells us, “But now in Christ Jesus ye who sometimes were far off are made nigh by the blood of Christ.” And it is only through His blood that this is possible.