Statements presented by mathworks website, these appear to be generally applicable.

Deciding Between ODBC and JDBC Drivers

Use native ODBC for:

• Fastest performance for data imports and exports
• Memory-intensive data imports and exports

Use JDBC for:

• Platform independence allowing you to work with any operating system (including Mac and Linux®), driver version, or bitness (32-bit or 64-bit)
• Using Database Toolbox functions not supported by the native ODBC interface (such as runstoredprocedure)
• Working with complex or long data types (e.g., LONG, BLOB, text, etc.)

Tip:

• On Windows systems that support both ODBC and JDBC drivers, pure JDBC drivers and the native ODBC interface provide better connectivity and performance than the JDBC/ODBC bridge.

The following points may help:

Multithread: - JDBC is multi-threaded - ODBC is not multi-threaded (at least not thread safe)

Flexibility: - ODBC is a windows-specific technology - JDBC is specific to Java, and is therefore supported on whatever OS supports Java

Power : you can do everything with JDBC that you can do with ODBC, on any platform.

Language: - ODBC is procedural and language independent - JDBC is object oriented and language dependent (specific to java).

Heavy load: - JDBC is faster - ODBC is slower

ODBC limitation: it is a relational API and can only work with data types that can be expressed in rectangular or two-dimensional format. (it will not work with data types like Oracle’s spatial data type)

API: JDBC API is a natural Java Interface and is built on ODBC, and therefore JDBC retains some of the basic feature of ODBC

Are you sure you are comparing drivers and not whole environments?

I see that for ODBC you use C program. Try ODBC driver with the same program you use to test JDBC but now use JDBC-ODBC bridge (I often use Jython for such things). Of course bridge adds some additional time. Also remember that JVM uses JIT -- the longer your application works the better performance.

Performance is important but for me much more important is stability of drivers. I had some problems with various ODBC drivers and now I prefer JDBC drivers. But even ODBC drivers can work with high-load multi-threaded servers for many months.