@jeevankoshy, you have asked an excellent question. Our consciences can be corrupted, so how do we know when we are hearing the truth of the Holy Spirit in us? God has given us the law written on our hearts as the apostle Paul states:
“For when Gentiles, who do not have the law, by nature do what the law requires, they are a law to themselves, even though they do not have the law. They show that the work of the law is written on their hearts, while their conscience also bears witness, and their conflicting thoughts accuse or even excuse them on that day when, according to my gospel, God judges the secrets of men by Christ Jesus.”
Romans 2:14-16 ESV
But we can more accurately know what the spirit of truth is when we read God’s word.
“So Jesus said to the Jews who had believed him, “If you abide in my word, you are truly my disciples,”
John 8:31 ESV
“Beloved, do not believe every spirit, but test the spirits to see whether they are from God, for many false prophets have gone out into the world. By this you know the Spirit of God: every spirit that confesses that Jesus Christ has come in the flesh is from God, and every spirit that does not confess Jesus is not from God. This is the spirit of the antichrist, which you heard was coming and now is in the world already. Little children, you are from God and have overcome them, for he who is in you is greater than he who is in the world. They are from the world; therefore they speak from the world, and the world listens to them. We are from God. Whoever knows God listens to us; whoever is not from God does not listen to us. By this we know the Spirit of truth and the spirit of error.”
1 John 4:1-6 ESV
Our consciences are given us by God as part of our thought processes to convict us as to what we believe is right or wrong. The Holy Spirit is God himself who dwells in Christians and guides us in truth.
Here is a good explanation of the difference between our consciences and the Holy Spirit:
Also, an article that describes our consciences from a christian perspective:
I hope some of this helps you understand these distinctions! God bless!