Jones is the former manager of Selby Town and left the Robins earlier this month after Boro's 2-1 victory at The Rigid Group Stadium.
He is a former trainee at Grimsby Town, had trials with both Bradford City and Lincoln City, and spent two years playing in the League of Ireland.
Jones has badges up to Level 2 and he managed at Boston Town reserves where he was promoted to first-team manager but decided to leave that role to become Selby boss.
A club statement said: "All at Grimsby Borough would like welcome Phil to the club and are so proud that they have been able to take on such a vast footballing knowledge in Phil."
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