How can I create an atmosphere/oxygen system in my 3d space game.

You can make this work as trigger volumes with dedicated component to represent sealed spaces. And script those changes in the environment (doors opening, fires etc) as changes to the oxygenLevel for given volumes.

Be pragmatic and make some gameplay first. Don't make this a voxelized fluid (gas) simulation project.

AtmosphericVolume.cs

 using UnityEngine;
 
 [RequireComponent( typeof(BoxCollider) )]
 public class AtmosphericVolume : MonoBehaviour
 {
     [Range(0,1)] public float oxygenLevel = 1;
 
     #if UNITY_EDITOR
     void OnValidate ()
     {
         var collider = GetComponent<BoxCollider>();
         if( !collider.isTrigger )
             Debug.LogWarning("make me a trigger human!", gameObject);
     }
     void OnDrawGizmos ()
     {
         var collider = GetComponent<BoxCollider>();
         if( collider!=null )
         {
             Gizmos.matrix = transform.localToWorldMatrix;
             Gizmos.color = oxygenLevel<1 ? Color.black : Color.white;
             Gizmos.DrawWireCube( collider.center , collider.size );
             Gizmos.color = new Color{ r=1f , g=1f , b=1f , a=0.05f };
             Gizmos.DrawCube( collider.center , collider.size );
         }
     }
     #endif
 }

BreathingPawn.cs

 using System.Collections.Generic;
 using UnityEngine;
 [RequireComponent( typeof(CapsuleCollider) )]
 [RequireComponent( typeof(Rigidbody) )]
 public class BreathingPawn : MonoBehaviour
 {
     // note: not a List but HashSet because it prevents duplication
     HashSet<AtmosphericVolume> _oxygenSources = new HashSet<AtmosphericVolume>();
     
     [SerializeField][Range(0,1)] float _oxygen = 1f;
     [SerializeField][Min(0)] float _oxygenReplenishment = 0.05f;
     [SerializeField][Min(0)] float _oxygenConsumption = 0.05f;
     [SerializeField] AnimationCurve _oxygenLevelViability = new AnimationCurve( new Keyframe(0,0,0,0) , new Keyframe(1,1,3.3f,0) );
     const float k_breathing_tick_rate = 1f / 3f;// 3 times per second
     void OnEnable ()
     {
         // This will create a custom Update-like function that will be called repeatedly.
         // I'm not using Update because breathing don't have to be calculated every time a frame is drawn (just wasteful)
         InvokeRepeating( nameof(Tick_Breathing) , time:k_breathing_tick_rate , repeatRate:k_breathing_tick_rate );
     }
     void OnTriggerEnter ( Collider other )
     {
         var comp = other.GetComponent<AtmosphericVolume>();
         if( comp!=null )
             _oxygenSources.Add(comp);
     }
     void OnTriggerExit ( Collider other )
     {
         var comp = other.GetComponent<AtmosphericVolume>();
         if( comp!=null )
             _oxygenSources.Remove(comp);
     }
     #if UNITY_EDITOR
     void OnDrawGizmos ()
     {
         Gizmos.color = Color.white;
         Vector3 pos = transform.position;
         foreach( var source in _oxygenSources )
             Gizmos.DrawLine( pos , source.transform.position );
     }
     #endif
     void Tick_Breathing ()
     {
         // in cases when atmo volumes overlap - pick the better one:
         float oxygenAround = 0f;
         foreach( var volume in _oxygenSources )
             oxygenAround = Mathf.Max( oxygenAround , volume.oxygenLevel );
         
         // breathing:
         float oxygenIntake = _oxygenReplenishment * k_breathing_tick_rate * _oxygenLevelViability.Evaluate(oxygenAround);
         _oxygen = Mathf.Clamp01( _oxygen + oxygenIntake );
 
         // oxygen consumption:
         float oxygenConsumed = _oxygenConsumption * k_breathing_tick_rate * ( 1f - oxygenAround );
         _oxygen = Mathf.Clamp01( _oxygen - oxygenConsumed );
         
         if( !(_oxygen>0) )
             OnAsphyxiation();
     }
     void OnAsphyxiation ()
     {
         Debug.Log($"{gameObject.name} is x__x (asphyxiation)",gameObject);
         gameObject.SetActive( false );
     }
 }